rm aliases to uhdas script

uhdas script cleanup

uhdas_00

-uhdas_00_linkmerge
\ No newline at end of file

uhdas_00

+#!/bin/csh -f
+#
+# bak in Amsterdam before start of jc184 uhdas trial
+# 3 July 2019
+#
+# 1) rsync uhdas data from uhdas server to local machine
+#
+# 2) ensure postprocessing directories exist
+#
+# If the script hasn't been run recently, there will 
+# be a lot of files to sync across. The processing on the uhdas
+# server updates plenty of things in routine processing every few minutes.
+# If the script is then immediately run again, there will be a few files
+# that are updated every ping.
+#
+# List of cruise segments to be processed is found in
+# ~/cruise/data/vmadcp/cruise_segments
+
+cd /local/users/pstar/cruise/data/vmadcp/spprocessing
+
+foreach i (`cat ~/cruise/data/vmadcp/cruise_segments`)
+echo linking ${i} to $1
+link_uhdaslegs.py ../atsea/${i} $1
+end
+
+if (! -e config) then
+mkdir config
+cp ../atsea/${i}/raw/config/*_proc.py config/$1_proc.py
+echo 'edit config/*proc.py cruiseid, uhdas_dir'
+endif
+

uhdas_00_linkmerge

-#!/bin/csh -f
-#
-# bak in Amsterdam before start of jc184 uhdas trial
-# 3 July 2019
-#
-# 1) rsync uhdas data from uhdas server to local machine
-#
-# 2) ensure postprocessing directories exist
-#
-# If the script hasn't been run recently, there will 
-# be a lot of files to sync across. The processing on the uhdas
-# server updates plenty of things in routine processing every few minutes.
-# If the script is then immediately run again, there will be a few files
-# that are updated every ping.
-#
-# List of cruise segments to be processed is found in
-# ~/cruise/data/vmadcp/cruise_segments
-
-cd /local/users/pstar/cruise/data/vmadcp/spprocessing
-
-foreach i (`cat ~/cruise/data/vmadcp/cruise_segments`)
-echo linking ${i} to $1
-link_uhdaslegs.py ../atsea/${i} $1
-end
-
-if (! -e config) then
-mkdir config
-cp ../atsea/${i}/raw/config/*_proc.py config/$1_proc.py
-echo 'edit config/*proc.py cruiseid, uhdas_dir'
-endif
-

uhdas_01

-uhdas_01_syncraw
\ No newline at end of file

uhdas_01

+#!/bin/csh -f
+#
+# bak in Amsterdam before start of jc184 uhdas trial
+# 3 July 2019
+#
+# 1) rsync uhdas data from uhdas server to local machine
+#
+# 2) ensure postprocessing directories exist
+#
+# If the script hasn't been run recently, there will 
+# be a lot of files to sync across. The processing on the uhdas
+# server updates plenty of things in routine processing every few minutes.
+# If the script is then immediately run again, there will be a few files
+# that are updated every ping.
+#
+# List of cruise segments to be processed is found in
+# ~/cruise/data/vmadcp/cruise_segments
+
+set rdir = ~/mounts/uhdas_data
+set ldir = ~/cruise/data/vmadcp
+
+mkdir -p ${ldir}/atsea
+mkdir -p ${ldir}/postprocessing
+
+foreach i (`cat ~/cruise/data/vmadcp/cruise_segments`)
+echo syncing ${i} to ${ldir}
+rsync -auv ${rdir}/${i} ${ldir}/atsea/
+
+mkdir -p ${ldir}/postprocessing/${i}/proc_editing
+mkdir -p ${ldir}/postprocessing/${i}/proc_archive
+end
+
+echo end of syncing ${i} to ${ldir}
+

uhdas_01_syncraw

-#!/bin/csh -f
-#
-# bak in Amsterdam before start of jc184 uhdas trial
-# 3 July 2019
-#
-# 1) rsync uhdas data from uhdas server to local machine
-#
-# 2) ensure postprocessing directories exist
-#
-# If the script hasn't been run recently, there will 
-# be a lot of files to sync across. The processing on the uhdas
-# server updates plenty of things in routine processing every few minutes.
-# If the script is then immediately run again, there will be a few files
-# that are updated every ping.
-#
-# List of cruise segments to be processed is found in
-# ~/cruise/data/vmadcp/cruise_segments
-
-set rdir = ~/mounts/uhdas_data
-set ldir = ~/cruise/data/vmadcp
-
-mkdir -p ${ldir}/atsea
-mkdir -p ${ldir}/postprocessing
-
-foreach i (`cat ~/cruise/data/vmadcp/cruise_segments`)
-echo syncing ${i} to ${ldir}
-rsync -auv ${rdir}/${i} ${ldir}/atsea/
-
-mkdir -p ${ldir}/postprocessing/${i}/proc_editing
-mkdir -p ${ldir}/postprocessing/${i}/proc_archive
-end
-
-echo end of syncing ${i} to ${ldir}
-

uhdas_02

-uhdas_02_sync_postprocessing_from_raw
\ No newline at end of file

uhdas_02

+#!/bin/csh -f
+#
+# bak in Amsterdam before start of jc184 uhdas trial
+# 3 July 2019
+#
+# 1) rsync proc directory from the local atsea copy to the editing directory
+#
+# If the script hasn't been run recently, there will 
+# be a lot of files to sync across. The processing on the uhdas
+# server updates plenty of things in routine processing every few minutes.
+# If the script is then immediately run again, there will be a few files
+# that are updated every ping.
+#
+# List of cruise segments to be processed is found in
+# ~/cruise/data/vmadcp/cruise_segments
+
+set ldir = ~/cruise/data/vmadcp
+
+
+foreach i (`cat ~/cruise/data/vmadcp/cruise_segments`)
+echo
+echo
+echo syncing 
+echo ${ldir}/atsea/${i}/proc 
+echo to 
+echo ${ldir}/postprocessing/${i}/proc_editing
+rsync -auv ${ldir}/atsea/${i}/proc/ ${ldir}/postprocessing/${i}/proc_editing/
+echo
+echo
+
+end
+

uhdas_02_sync_postprocessing_from_raw

-#!/bin/csh -f
-#
-# bak in Amsterdam before start of jc184 uhdas trial
-# 3 July 2019
-#
-# 1) rsync proc directory from the local atsea copy to the editing directory
-#
-# If the script hasn't been run recently, there will 
-# be a lot of files to sync across. The processing on the uhdas
-# server updates plenty of things in routine processing every few minutes.
-# If the script is then immediately run again, there will be a few files
-# that are updated every ping.
-#
-# List of cruise segments to be processed is found in
-# ~/cruise/data/vmadcp/cruise_segments
-
-set ldir = ~/cruise/data/vmadcp
-
-
-foreach i (`cat ~/cruise/data/vmadcp/cruise_segments`)
-echo
-echo
-echo syncing 
-echo ${ldir}/atsea/${i}/proc 
-echo to 
-echo ${ldir}/postprocessing/${i}/proc_editing
-rsync -auv ${ldir}/atsea/${i}/proc/ ${ldir}/postprocessing/${i}/proc_editing/
-echo
-echo
-
-end
-

uhdas_03

-uhdas_03_copy_asclog_for_editing
\ No newline at end of file

uhdas_03

+#!/bin/bash
+#
+# bak in Amsterdam before start of jc184 uhdas trial
+# 3 July 2019
+#
+# This is run as a bash, because we want the quick_adcp.py to run in the
+# python 3 environment
+# 
+# This script merges the edits stored in the proc_archive asclog file with 
+# any stored in the proc_editing file
+#
+# The combined sorted edits are stored in both of asc and asclog in the proc_editing file
+# The editing process takes past input from .asc, and appends new edits to .asclog
+#
+# List of cruise segments to be processed is found in
+# ~/cruise/data/vmadcp/cruise_segments
+#
+
+# make sure the bash environment is set up
+source ~/.bashrc
+
+# no set command in bash
+ldir=~/cruise/data/vmadcp
+
+for segname in `cat ~/cruise/data/vmadcp/cruise_segments`
+do
+
+pushd ${ldir}/postprocessing/${segname}/proc_editing
+
+
+for pingtype in `ls -d *`
+do
+echo ${segname}/${pingtype}
+data=0
+if test -f ${ldir}/postprocessing/${segname}/proc_editing/${pingtype}/adcpdb/*dir.blk
+then
+data=1
+fi
+
+echo data ${data}
+
+if [ ${data} -eq  1 ]
+then
+pushd ${ldir}/postprocessing/${segname}/proc_editing/${pingtype}
+thisdir=`pwd`
+echo working in ${thisdir}
+
+# now fix the asc files
+
+for asctype in abadbin abottom abadprf
+do
+echo ${asctype}
+f1=${ldir}/postprocessing/${segname}/proc_editing/${pingtype}/edit/${asctype}.asclog
+f2=${ldir}/postprocessing/${segname}/proc_archive/${pingtype}/edit/${asctype}.asclog
+f3=${ldir}/postprocessing/${segname}/proc_editing/${pingtype}/edit/${asctype}.asc
+f4=${ldir}/postprocessing/${segname}/proc_editing/${pingtype}/edit/${asctype}.asclog
+cat ${f1} ${f2} | sort -u > ${f3}
+/bin/cp -p ${f3} ${f4}
+done
+
+thisdir=`pwd`
+echo quick_adcp.py in ${thisdir}
+which quick_adcp.py
+quick_adcp.py --steps2rerun apply_edit:navsteps:calib --auto
+
+
+popd
+fi
+done
+popd
+
+
+done

uhdas_03_copy_asclog_for_editing

-#!/bin/bash
-#
-# bak in Amsterdam before start of jc184 uhdas trial
-# 3 July 2019
-#
-# This is run as a bash, because we want the quick_adcp.py to run in the
-# python 3 environment
-# 
-# This script merges the edits stored in the proc_archive asclog file with 
-# any stored in the proc_editing file
-#
-# The combined sorted edits are stored in both of asc and asclog in the proc_editing file
-# The editing process takes past input from .asc, and appends new edits to .asclog
-#
-# List of cruise segments to be processed is found in
-# ~/cruise/data/vmadcp/cruise_segments
-#
-
-# make sure the bash environment is set up
-source ~/.bashrc
-
-# no set command in bash
-ldir=~/cruise/data/vmadcp
-
-for segname in `cat ~/cruise/data/vmadcp/cruise_segments`
-do
-
-pushd ${ldir}/postprocessing/${segname}/proc_editing
-
-
-for pingtype in `ls -d *`
-do
-echo ${segname}/${pingtype}
-data=0
-if test -f ${ldir}/postprocessing/${segname}/proc_editing/${pingtype}/adcpdb/*dir.blk
-then
-data=1
-fi
-
-echo data ${data}
-
-if [ ${data} -eq  1 ]
-then
-pushd ${ldir}/postprocessing/${segname}/proc_editing/${pingtype}
-thisdir=`pwd`
-echo working in ${thisdir}
-
-# now fix the asc files
-
-for asctype in abadbin abottom abadprf
-do
-echo ${asctype}
-f1=${ldir}/postprocessing/${segname}/proc_editing/${pingtype}/edit/${asctype}.asclog
-f2=${ldir}/postprocessing/${segname}/proc_archive/${pingtype}/edit/${asctype}.asclog
-f3=${ldir}/postprocessing/${segname}/proc_editing/${pingtype}/edit/${asctype}.asc
-f4=${ldir}/postprocessing/${segname}/proc_editing/${pingtype}/edit/${asctype}.asclog
-cat ${f1} ${f2} | sort -u > ${f3}
-/bin/cp -p ${f3} ${f4}
-done
-
-thisdir=`pwd`
-echo quick_adcp.py in ${thisdir}
-which quick_adcp.py
-quick_adcp.py --steps2rerun apply_edit:navsteps:calib --auto
-
-
-popd
-fi
-done
-popd
-
-
-done

uhdas_04

-uhdas_04_export_nc
\ No newline at end of file

uhdas_04

+#!/bin/bash
+#
+# bak in Amsterdam before start of jc184 uhdas trial
+# 3 July 2019
+#
+# This is run as a bash, because we want the adcp_nc.py to run in the
+# python 3 environment
+# 
+# This script remakes the contour/os150nb.nc file after dataviewer editing
+#
+# List of cruise segments to be processed is found in
+# ~/cruise/data/vmadcp/cruise_segments
+#
+
+# make sure the bash environment is set up
+source ~/.bashrc
+
+# no set command in bash
+ldir=~/cruise/data/vmadcp
+
+for segname in `cat ~/cruise/data/vmadcp/cruise_segments`
+do
+
+pushd ${ldir}/postprocessing/${segname}/proc_editing
+
+
+for pingtype in `ls -d *`
+do
+echo ${segname}/${pingtype}
+data=0
+if test -f ${ldir}/postprocessing/${segname}/proc_editing/${pingtype}/adcpdb/*dir.blk
+then
+data=1
+fi
+
+echo data ${data}
+
+if [ ${data} -eq  1 ]
+then
+pushd ${ldir}/postprocessing/${segname}/proc_editing/${pingtype}
+thisdir=`pwd`
+echo working in ${thisdir}
+
+
+thisdir=`pwd`
+echo adcp_nc.py in ${thisdir}
+which adcp_nc.py
+adcp_nc.py adcpdb contour/${pingtype} dy120 ${pingtype}
+
+thisdir=`pwd`
+echo quick_adcp.py in ${thisdir}
+which quick_adcp.py
+quick_adcp.py --steps2rerun matfiles --auto
+
+popd
+fi
+done
+popd
+
+
+done

uhdas_04_export_nc

-#!/bin/bash
-#
-# bak in Amsterdam before start of jc184 uhdas trial
-# 3 July 2019
-#
-# This is run as a bash, because we want the adcp_nc.py to run in the
-# python 3 environment
-# 
-# This script remakes the contour/os150nb.nc file after dataviewer editing
-#
-# List of cruise segments to be processed is found in
-# ~/cruise/data/vmadcp/cruise_segments
-#
-
-# make sure the bash environment is set up
-source ~/.bashrc
-
-# no set command in bash
-ldir=~/cruise/data/vmadcp
-
-for segname in `cat ~/cruise/data/vmadcp/cruise_segments`
-do
-
-pushd ${ldir}/postprocessing/${segname}/proc_editing
-
-
-for pingtype in `ls -d *`
-do
-echo ${segname}/${pingtype}
-data=0
-if test -f ${ldir}/postprocessing/${segname}/proc_editing/${pingtype}/adcpdb/*dir.blk
-then
-data=1
-fi
-
-echo data ${data}
-
-if [ ${data} -eq  1 ]
-then
-pushd ${ldir}/postprocessing/${segname}/proc_editing/${pingtype}
-thisdir=`pwd`
-echo working in ${thisdir}
-
-
-thisdir=`pwd`
-echo adcp_nc.py in ${thisdir}
-which adcp_nc.py
-adcp_nc.py adcpdb contour/${pingtype} jc191 ${pingtype}
-
-thisdir=`pwd`
-echo quick_adcp.py in ${thisdir}
-which quick_adcp.py
-quick_adcp.py --steps2rerun matfiles --auto
-
-popd
-fi
-done
-popd
-
-
-done

uhdas_05

-uhdas_05_sync_edited_to_archive
\ No newline at end of file

uhdas_05

+#!/bin/csh -f
+#
+# bak in Amsterdam before start of jc184 uhdas trial
+# 3 July 2019
+#
+# 1) rsync proc_edited directory back to proc_archive after editing with dataviewer.py -e
+#
+
+# List of cruise segments to be processed is found in
+# ~/cruise/data/vmadcp/cruise_segments
+#
+set ldir = ~/cruise/data/vmadcp
+#
+#
+foreach i (`cat ~/cruise/data/vmadcp/cruise_segments`)
+echo
+echo
+echo syncing 
+echo ${ldir}/postprocessing/${i}/proc_editing
+echo to 
+echo ${ldir}/postprocessing/${i}/proc_archive
+rsync -av ${ldir}/postprocessing/${i}/proc_editing/ ${ldir}/postprocessing/${i}/proc_archive/
+echo
+echo
+#
+end
+#
+
+
+
+
+

uhdas_05_sync_edited_to_archive

-#!/bin/csh -f
-#
-# bak in Amsterdam before start of jc184 uhdas trial
-# 3 July 2019
-#
-# 1) rsync proc_edited directory back to proc_archive after editing with dataviewer.py -e
-#
-
-# List of cruise segments to be processed is found in
-# ~/cruise/data/vmadcp/cruise_segments
-#
-set ldir = ~/cruise/data/vmadcp
-#
-#
-foreach i (`cat ~/cruise/data/vmadcp/cruise_segments`)
-echo
-echo
-echo syncing 
-echo ${ldir}/postprocessing/${i}/proc_editing
-echo to 
-echo ${ldir}/postprocessing/${i}/proc_archive
-rsync -av ${ldir}/postprocessing/${i}/proc_editing/ ${ldir}/postprocessing/${i}/proc_archive/
-echo
-echo
-#
-end
-#
-
-
-
-
-

uhdas_linkscript

+#!/bin/csh -f
+#
+# wrapper script for uhdas
+# 2020, LOH on dy120
+#
+
+uhdas_01
+uhdas_02
+uhdas_03
+# if manual editing is needed:
+# cd proc_editing; cd osXXnb; bash; dataviewer.py -e;
+uhdas_04
+uhdas_05