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 ##
 ## Copyright (c) 2019 Opticks Team. All Rights Reserved.
 ##
 ## This file is part of Opticks
 ## (see https://bitbucket.org/simoncblyth/opticks).
 ##
 ## Licensed under the Apache License, Version 2.0 (the "License"); 
 ## you may not use this file except in compliance with the License.  
 ## You may obtain a copy of the License at
 ##
 ##   http://www.apache.org/licenses/LICENSE-2.0
 ##
 ## Unless required by applicable law or agreed to in writing, software 
 ## distributed under the License is distributed on an "AS IS" BASIS, 
 ## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.  
 ## See the License for the specific language governing permissions and 
 ## limitations under the License.
 ##
 
 ana-rel(){      echo ana ; }
 ana-src(){      echo ana/ana.bash ; }
 ana-source(){   echo ${BASH_SOURCE:-$(opticks-home)/$(ana-src)} ; }
 ana-vi(){       vi $(ana-source) ; }
 ana-usage(){ cat << \EOU
 
 ana : Opticks Analysis Scripts
 =================================
 
 
 Issue : analysis machinery expects a geocache
 ---------------------------------------------------
 
 ::
 
     simon:analytic blyth$ ip
     Python 2.7.11 (default, Dec  5 2015, 23:51:51) 
     ...
     IPython profile: g4opticks
     args: /opt/local/bin/ipython 
     Invalid/missing IDPATH envvar /usr/local/opticks/opticksdata/export/DayaBay_VGDX_20140414-1300/g4_00.96ff965744a2f6b78c24e33c80d3a4cd.dae 
     An exception has occurred, use %tb to see the full traceback.
 
     SystemExit: 1
 
     To exit: use 'exit', 'quit', or Ctrl-D.
 
     In [1]: 
 
 
 
 FUNCTION `ana-t`
 ------------------
 
 After running `tests-t` all the below "MISSING EVT" should become "OK"::
 
     simon:ana blyth$ ana-t
     ==                    __init__.py ==  ->    0 OK  
     ==                         ana.py ==  ->  101 MISSING EVT  
     ==                        base.py ==  ->    0 OK  
     ==                    boundary.py ==  ->    0 OK  
     ==              cfg4_speedplot.py ==  ->    0 OK  
     ==                      cfplot.py ==  ->    0 OK  
     ==                         cie.py ==  SKIP
     ==                     dbgseed.py ==  ->  101 MISSING EVT  
     ==                     droplet.py ==  ->    0 OK  
     ==                         evt.py ==  ->    0 OK  
     ==                     fresnel.py ==  ->    0 OK  
     ==                       g4gun.py ==  ->  101 MISSING EVT  
     ==                     genstep.py ==  ->    0 OK  
     ==                    geometry.py ==  ->    0 OK  
     ==                     histype.py ==  ->    0 OK  
     ==                    material.py ==  ->    0 OK  
     ==                     mattype.py ==  ->    0 OK  
     ==                  mergedmesh.py ==  ->    0 OK  
     ==                    metadata.py ==  ->    0 OK  
     ==                       nbase.py ==  ->    0 OK  
     ==                     ncensus.py ==  ->    0 OK  
     ==                       nload.py ==  ->    0 OK  
     ==                          ox.py ==  ->    0 OK  
     ==                      planck.py ==  ->    0 OK  
     ==              prism_spectrum.py ==  ->  101 MISSING EVT  
     ==                     proplib.py ==  ->    0 OK  
     ==                         seq.py ==  ->    0 OK  
     ==                      sphere.py ==  ->  101 MISSING EVT  
     ==                        tbox.py ==  ->  101 MISSING EVT  
     ==                        tevt.py ==  ->  101 MISSING EVT  
     ==                       tmeta.py ==  ->    0 OK  
     ==                        tpmt.py ==  ->  101 MISSING EVT  
     ==                tpmt_distrib.py ==  ->  101 MISSING EVT  
     ==                tpmt_skimmer.py ==  ->  101 MISSING EVT  
     ==                      tprism.py ==  ->  101 MISSING EVT  
     ==                    trainbow.py ==  ->  101 MISSING EVT  
     ==                    treflect.py ==  ->  101 MISSING EVT  
     ==                      twhite.py ==  ->  101 MISSING EVT  
     ==                    xrainbow.py ==  ->    0 OK  
 
 
 
 PMT Tests
 ------------
 
 :doc:`tpmt`
     Compare Opticks and Geant4 photon bounce histories for simple PMT in box of mineral oil geometry,
     see :doc:`../tests/tpmt`
 
 :doc:`tpmt_distrib`
     Compare Opticks and Geant4 photon distributions for simple PMT in box of mineral oil geometry 
 
 :doc:`tpmt_skimmer`
     Plotting and tabulating mean step by step positions of all photons with specific step histories 
     such as "TO BT BT SA" 
 
 
 BoxInBox tests
 ------------------
 
 :doc:`tbox`
     BoxInBox Opticks vs Geant4 history sequence comparisons analogous to **tpmt.py**
     see :doc:`../tests/tbox`
 
 **tboxlaser.py**
     Looks like simple event comparison, without using AB/CF etc..
     TODO: use the generic AB machinery to do the same
 
 
 Rainbow Tests
 ---------------
 
 :doc:`trainbow`
     Rainbow scattering angle comparison between Opticks and Geant4,
     see :doc:`../tests/trainbow`
 
 **xrainbow.py**
     Rainbow expectations with classes XRainbow and XFrac
 
 **droplet.py**
     geometry calculation of spherical drop incident, refracted, 
     deviation angles for k orders of rainbow corresponding to different numbers
     of internal reflections
 
 **sphere.py**
     SphereReflect intersection, polarization calculation and spatial plot
 
 
 Scatter Tests
 ---------------
 
 **rayleigh.py**
     Without selection scatter distrib plots from arrays created by:
 
     optixrap/tests/ORayleighTest.cc 
     cfg4/tests/OpRayleighTest.cc
 
 
 Source Tests
 --------------
 
 :doc:`twhite`
     Compare wavelength spectrum from :doc:`../tests/twhite` against analytic Planck distribution
 
 **planck.py**
     Planck black body formula : CDF technique dev, plotting
 
 
 Full Geometry Tests
 ----------------------
 
 **tdefault.py**
      tests within default full geometry, using CF (older than the AB/CFH machinery?)
 
 **tdefault_distrib.py**
      tests within default full geometry, using cf,cfplot
 
 **tlaser.py**
      okg4 comparisons manually using Evt (not the newer AB)
 
 **tlaser_distrib.py**
      okg4 comparisons using CF (not the newer CFH)
 
 
 Analytic/NCSG Geometry tests
 -----------------------------
 
 **analytic_boundary_dbg.py**
     analysis of photon_buffer written by oxrap/cu/generate.cu:tracetest
 
     TODO: rename, too special case to share name with tboolean-   
 
 **tgltf.py** 
     Shakedown analytic geometry, with analytic geometry transform access
 
 Concentric Tests : idealised spherical DYB AD
 ----------------------------------------------
 
 **tconcentric.py**
      comparison using AB, with scatter polarization debug/plotting
      see tconcentric-i
 
 **tconcentric_distrib.py**
      comparison histo mass production with 
      see tconcentric-d
 
 
 Lens/Prism Tests
 ------------------
 
 **tlens.py**
     Single Evt dumping, no comparisons
 
 **tprism.py**
     Comparison of simulation with analytic expectations for deviation angle vs incident angle,
     see :doc:`../tests/tprism`
 
 **prism_spectrum.py**
     Compare ggv-newton evts with PrismExpected
 
 
 Reflection Tests
 ------------------- 
 
 **treflect.py**
     comparison of simulated S and P absolute reflection with Fresnel formula 
     see :doc:`../tests/treflect`
 
 **fresnel.py**
     analytic reflection expectations from Fresnel formula
 
 
 G4Gun Tests
 --------------
 
 :doc:`g4gun`
     Load single G4Gun event
 
 
 Geometry Infrastructure 
 -------------------------
 
 :doc:`material`
     Material class gives access to geocache material properties 
 
 :doc:`boundary`
     Boundary class acts as holder of inner/outer materials and surfaces
 
 :doc:`proplib`
     Access to geocache via PropLib
 
 **bnd.py**
     testing PropLib usage to access material and surface properties
  
 :doc:`mergedmesh`
     Access geometrical data such as positions, transforms of volumes of the geometry
 
 **geometry.py**
     Shape, Ray, Plane, Intersect, IntersectFrame : simple intersect calulations
 
 
 
 Event Comparison Infrastructure
 -----------------------------------
 
 **tokg4.py**
     loads evt pair and compares at Evt level
 
 **ab.py**
     event pair comparison with AB class. Used by cfh.py, cfplot.py, tconcentric.py, tconcentric_distrib.py
 
 **abstat.py**
     history table slicing, selection. Used by ab.py, cfh.py
 
 **make_rst_table.py**
     pure python utility used by ab.py abstat.py 
 
 **cf.py**
     Sliced history CF spawning.      
     Used by tdefault.py tdefault_distrib.py tlaser_distrib.py tpmt_distrib.py
 
 **decompression.py**
     Deco : utils for re-binning domain compressed values that avoid binning artifacts
 
     Used from : ab.py cf.py 
 
   
 **cfh.py**
     CFH : persistable comparison histograms and chi2, with random access via path specification
 
     ipython -i $(which cfh.py) -- /tmp/blyth/opticks/CFH/concentric/1/TO_BT_BT_BT_BT_SA/0/X
 
     Used from : ab.py cf.py cfhload.py cfplot.py tconcentric.py 
 
 **cfhload.py**
     Testing cfh.py CFH
 
 **ctx.py**
     Ctx : Utility providing conversions between various ways of addressing comparison histograms
 
     Used from : ab.py cfh.py evt.py
 
 
 Event Infrastructure
 -----------------------
 
 :doc:`tevt`
     Loads single event and dumps constituent array dimensions and photon history tables
 
 **evt.py**
     loads event data : used by many ~30 other scripts
 
 **tmeta.py**
     loads and dumps a single events metadata 
 
     tmeta.py --det tboolean-torus --tag 1
 
 
 **base.py** 
     internal envvar setup based on input envvar IDPATH 
     json and ini loading with Abbrev and ItemList classes 
 
 **ok.py** 
     test of opticks_main arg parsing/defaults  
 
 **enum.py** 
     parsing C++ enum into python dict. Used by base.py 
  
 **nload.py**
     numpy array and .ini metadata loading with clases A, I, II
 
 **ox.py**
     load just final photons, testing nload and arg parsing  
 
 **ph.py**
     load ph photon seqhis, dumping progressing SeqAna sequences
 
 
 **nbase.py**
     pure numpy utility functions: count_unique, count_unique_sorted, chi2, decompression_bins 
 
 **seq.py**
     SeqType conversions of long integer sequence codes to abbreviation string sequences like  "TO BT BR BR BT SA"
     SeqTable presenting frequencies of different sequences 
 
     Used by : evt.py hismask.py histype.py mattype.py
 
 **histype.py**
     HisType (SeqType subclass) and tests of history table formation and dumping.
     Used by ab.py cf.py evt.py seq.py. With entry point::
 
         histype.py --det tboolean-torus --tag -1 --src torch 
 
 **hismask.py**
     converts seqhis into a mask, not the usual sequence : used by evt.py pflags.py
 
         
 **mattype.py**
     MatType (SeqType subclass) and tests
 
 **genstep.py** 
     fit genstep xyz vs time, to obtain parametric eqn for the viewpoint tracking 
     used to create videos, see `vids-`
 
 **genstep_merge.py** 
     combine Cerenkov and scintillation gensteps in natural ones
 
 
 **ana.py**
     geometrical and plotting utils
 
 **OpticksQuery.py**
     analog of okc/OpticksQuery.cc geometry selection string parsing available from opticks_main args.query 
 
 
 
 Plotting Infrastructure
 --------------------------
 
 **cfplot.py**
     Comparison Plotter with Chi2 Underplot 
 
 
 Metadata Infrastructure
 --------------------------
 
 **cfg4_speedplot.py**
     compare simulation times using json metadata written by Opticks simulation invokations
 
 **metadata.py** 
     access metadata .json written by Opticks allowing 
     comparisons of evt digests and simulation times 
 
 **ncensus.py**
     event census looking across many events with array shape dumping 
 
 
 Color Infrastructure
 ----------------------
 
 **cie.py**
     converts wavelength spectra into XYZ and RGB colorspace (depends on **env** repo)
 
 
 
 EOU
 }
 
 ana-notes(){ cat << EON
 
 DEBUGGING SCRIPTS : NOT SURFACING THESE IN THE DOCS
 ------------------------------------------------------
 
 types.py
      MOSTLY DEPRECATED : INSTEAD USE histype mattype ETC
 
 analytic_cf_triangulated.py
      plotting analytic PMT and mesh points together
 
 nopstep_viz_debug.py
      creates fake nopstep (non-photon step) for visualization debugging
 
 mm_buffer.py 
      debugging mesh buffer structure
 
 
 dae.py
      simple XML COLLADA parsing of .dae for debugging 
 
 xmatlib.py
      COLLADA XML material properties access for debugging
 
 groupvel.py
      debug in progress
 
 genstep_sequence_material_mismatch.py
      dbg 
 
 CGDMLDetector.py
      access to global transforms obtained from GDMLDetector  
 
 instancedmergedmesh.py
      debugging of instanced mesh info such as PMT meshes  
 
 vacuum_offset.py
      geometry debug, the sagging vacuum
 
 IndexerTest.py
      debug small GPU CPU indexing differences 
 
 polarization.py
      checking magnitude of polarization for Opticks and G4 rainbow events
 
 ana.py
      misc old analysis funcs. Used from tprism.py, treflect.py
 
 cf5d.py
      5d Proplib comparison (dev code ?)
 
 dat.py 
      Dat : For interactive exploration of dimension > 3  arrays
 
 dbgseed.py
      old dev script used from oks-dbgseed
 
 gltf.py
      dev exploration of precision of transforms parsed from GLTF geometry json files
 
 gs.py
      example of pure numpy dumping of opticks buffers
 
 nodelib.py 
      check analytic and triangulates LVNames, PVNames lists 
 
 old_cfplot.py
      looks ancient
 
 pflags.py
      debugging inconsistent pflags in CFG4 evt
 
 seqmat.py
      debugging seqmat mismatch, zeros.
 
 truncation.py
      pseudo duplication of oxrap/cu/generate.cu for easy thinking about truncation
      and thinking about seqhis steered propagations 
 
 
 
 EON
 }
 ana-env(){
     olocal-
     opticks-
 }
 ana-sdir(){ echo $(opticks-home)/ana ; }
 ana-cd(){   cd $(ana-sdir); }
 
 ana-py-(){
    ana-cd
    ls -1 *.py 
 }
 
 ana-skips-note(){ cat << EON
 *ana-skips* 
     list .py scripts without executable bit set.
 
     Known fails, for example due to *env* repo dependency  
     can be skipped from ana-test simply by removing
     the executable bit::
 
         chmod ugo-x cie.py  
 
 EON
 }
 ana-skips(){
    local py
    ana-py- | while read py ; do
       [ ! -x $py ] && echo $msg SKIP $py 
    done
 }
 
 ana-t-note(){ cat << EON
 *ana-t*
      runs all executable .py in ana directory, 
      stopping at any script that yields a return code 
      that is not zero or 101
 
      Return code 101 is used to signal missing simulated evts 
 
      Use to check for simple python breakages from moving 
      things around for example. 
 
      Intended to just test mechanics, not meaning.
      Failure to load events should not cause failures, just warnings.
 EON
 }
 
 ana-t-rcm()
 {
    case $1 in 
      0)  echo OK ;;
    101)  echo MISSING EVT ;;  
      *)  echo PY FAIL ;;
    esac
 }
 
 ana-t(){
    local py
    local rc
    local rcm
    ana-cd
    ana-py- | while read py ; do
 
        printf "== %30s == " $msg $py
 
        [ ! -x $py ] && printf " SKIP\n" && continue
 
        ./$py > /dev/null 2>&1
        rc=$?
        rcm="$(ana-t-rcm $rc)"
        printf " -> %4s %s  \n" $rc "$rcm"
 
        if [ "$rc" == "0" -o "$rc" == "101" ]; then 
            echo -n
        else
            echo $msg WARNING : PY FAILURE OF $py : RC $rc
            break 
        fi
    done   
 }
 
 
 ana-shim(){
   ana-cd 
   local py
   local rst
   local name
   ls -1  t*.py | while read py ; do
       rst=${py/.py}.rst
       if [ ! -f "$rst" ];  then
           echo $msg writing rst shim $rst shim 
           ana-shim- $py > $rst 
       fi
   done 
 }
 
 ana-shim-(){ cat << EOR 
 
 .. include:: ${1:-dummy} 
    :start-after: """
    :end-before: """
 
 EOR
 }
 
 
 ana-pyref-(){ ana-usage | perl -n -e "m,(\w*\.py), && print \"\$1\n\"" | uniq ; }
 ana-pyref(){
    ana-cd
    local py
    ana-pyref- | while read py ; do
        [ ! -f "$py" ] && echo $msg bad pyref $py 
        printf " py %30s \n" $py  
    done 
 }
 
 ana-docref-(){ ana-usage | perl -n -e "m,:doc:\`(.*)\`, && print \"\$1\n\"" | uniq ; }
 ana-docref(){
    ana-cd
    local doc
    local rst
    ana-docref- | while read doc ; do
        rst=$doc.rst
        [ ! -f "$rst" ] && echo $msg BAD DOC REF $rst 
        printf " doc %30s rst %30s \n" $doc $rst  
    done 
 }
 
 ana-usage-refcheck-note(){ cat << EON
 **ana-usage-refcheck**
     check **ana-usage** for broken py and doc references 
 EON
 }
 ana-usage-refcheck()
 {
    ana-pyref
    ana-docref
 }
 
 
 ana-rstcheck()
 {
    ana-cd
    local rst
    local py
    grep  -l include:: *.rst | grep -v index.rst | while read rst ; do
        py=${rst/.rst}.py
        [ ! -f "$py" ] && echo $msg dud include $rst   
    done
 
 }
 
 
 
 
 ana-mod-ls-()
 {  
    ana-cd 
    ls -1 *.py
 }
 
 ana-mod-from()
 {
    local module
    ana-mod-ls- | while read module 
    do
        ana-mod-from- ${module/.py} 
    done
 }
 
 ana-mod-from-()
 {
    local msg="=== $FUNCNAME : "
    local module=${1:-cf}
    #echo
    echo $msg module $module used from :
    ana-cd
    $FUNCNAME- $module
 }
 
 ana-mod-from--()
 {
     grep -l from\ opticks.ana.${1:-cf}\  *.py 
 }

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