read.m will still work, but to use load_raw, must have set up these files (0) make directories to hold stuff assume: raw/ binfiles/ gbinfiles are all in the same root directory, easiest if inside adcp/ (i.e. parallel to adcpdb/, nav/, edit/,...) - linking is a perfectly reasonable way to get there raw/ raw/adcp_pings raw/adu2 raw/gyro raw/pcode raw/sndspd make these: binfiles/ binfiles/adu2 binfiles/gyro binfiles/pcode binfiles/sndspd gbinfiles/ gbinfiles/adu2 gbinfiles/gyro gbinfiles/pcode gbinfiles/sndspd gbinfiles/time (1) have to set up all the .bin files cd raw/pcode serasc2bin.py -o ../../binfiles/pcode *.gps cd ../adu2 serasc2bin.py -o ../../binfiles/adu2 *.adu cd ../gyro serasc2bin.py -o ../../binfiles/gyro *.hdg cd ../sndspd serasc2bin.py -o ../../binfiles/sndspd *.spd cd .. (2) for each adcp_pings/*.raw, have to make all the gbin files - they are expected to end up in the directories: [adu2, gyro, pcode, sndspd, time] - defaults are set to run from the root directory that contains raw/, binfiles/, and /gbinfiles - gps2bin; xxx2gbin(rawfilebase, 'binfpath', 'gyro') - (can run mk_allgbin from this root directory) ### example for vg0104 ### set cruiseid = vg0104 set dbname = a0104 set rawdir = '..'; set demo = /home/noio/programs/codas3/adcp/vmdas_demos/lta_demo/load (3) ## set up the cruise directory adcptree vg0104 /home/noio/programs/matlab cd vg0104 ln -s $rawdir/gbinfiles . ln -s $rawdir/raw . ## copy these files to load/ subdirectory cp -p $demo/ldcodas.cnt load cp -p $demo/load_lta.m load cp -p $demo/load_lta_manual.m load cp -p $demo/vmadcp.def load ## now we have gbinfiles alongside ping/ adcpdb/ and all the rest (4)# scan: get all timeranges for instance, do this from adcp/scan to get a file (alltimes.asc) %% do this in matlab tr2ilist([], 'gbinpath','../gbinfiles/time', ... 'file_exten', 'tim',... 'ascii_file', 'alltimes.scn'); (5) ## load (5a) ##editing and ping-averaging: %%in matlab; edit and run load_pings.m cd load load_pings %%see appendix (5b) ## load: ## edit ldcodas.cnt to contain the appropriate list of "*.cmd" files ## command line: run: ldcodas ldcodas.cnt (6) ## up for quick_adcp.prl (6a) ## replicate ubprint by creating a0104.ags cd ../nav cat ../load/*.gps1 > lta.gps1 cat ../load/*.gps2 > lta.gps2 ## for quick_adcp.prl to be happy: ln -s lta.gps1 ${dbname}.ags (6b) ## replicate the time range file (need a better scheme than this!!) cd ../load set tr = ../scan/${dbname}.tr set file1 = `ls *cmd | head -1` grep new_profile $file1 | head -1 | awk '{printf("%s %s", $2, $3)}' >> $tr echo -n " to " >> $trfile set file2 = `ls *cmd | tail -1` grep new_profile $file2 | tail -1 | awk '{printf("%s %s\n", $2, $3)}' >> $tr (7) ## now run quick_adcp.prl cd .. quick_adcp.prl -yearbase 2001 -noashtech -rlstart 3 -rlend 15 -progdir /home/ulili/programs -zapsetup (it says:) (you say) (what you're doing) Proceed with this dbname? (y/n/q) y (accept database) setup.m exists; make basic setup.m again? (y/n/q) y (make new setup.m) Proceed with ubprint? (y/n/q) n (do not run ubprint) Proceed to rotate? (y/n/q) y Proceed with adcpsect? (y/n/q) y Proceed with refabs? (y/n/q) y Proceed with smoothr? (y/n/q) y Proceed with putnav? (y/n/q) y Proceed with adcpsect (for autoedit)? (y/n/q) y Proceed with water track calibration? (y/n/q) y Proceed with bottom track calibration? (y/n/q) y list temperature? (y/n/q) y set up autoedit files? (y/n/q) y make matlab files?? (y/n/q) y edit/ autoedit list %reapply editing dbupdate ../adcpdb/atest abottom.asc dbupdate ../adcpdb/atest abadprf.asc badbin ../adcpdb/atest abadbin.asc set_lgb ../adcpdb/atest setflags setflags.tmp nav/ %rerun navsteps adcpsect as_nav.tmp refabs refabs.tmp smoothr smoothr.tmp putnav putnav.tmp %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% rotation is not getting in right amplitude is bad too: unedited: 11 points edited: 11 points, 2.0 min speed, 2.5 max dev median mean std amplitude 1.7088 1.7431 0.0699 phase -43.7810 -46.1751 6.0069 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% also ran into an error here. 0 out of 20 (../raw/adcp_pings/nbp2001_206_43200.raw) closing the att bin file ./nbp2001_206_43200.attstats.bin starting a new configuration segment: resetting leftover to [] calculating iranges 1 out of 4 (../raw/adcp_pings/nbp2001_206_49231.raw) 1 out of 293 bad headings in ensemble elapsed_time = 2.1785 2 out of 4 (../raw/adcp_pings/nbp2001_206_49231.raw) elapsed_time = 2.1767 3 out of 4 (../raw/adcp_pings/nbp2001_206_49231.raw) elapsed_time = 2.1939 4 out of 4 (../raw/adcp_pings/nbp2001_206_49231.raw) closing the att bin file ./nbp2001_206_49231.attstats.bin calculating iranges 1 out of 25 (../raw/adcp_pings/nbp2001_206_50400.raw) ??? Error using ==> - Matrix dimensions must agree. Error in ==> /home/ulili/programs/matlab/rawadcp/att_stats.m On line 43 ==> m_dh = abs(dh - bl_filt(dh, 20)) > c.max_dh_dev; Error in ==> /home/ulili/programs/matlab/rawadcp/rdi/@nb/load_raw.m On line 337 ==> [attstats, att_rownames] = att_stats(aux); -------------------------- 2002/01/08 got to here ------------------ ### encapsulated in get_rndata finfo = tr2ilist(allfinfo{4,2} + [0 300/86400], 'gbinpath','gbinfiles'); fullrawfile = fullfile('adcp_pings',finfo{1}); ilist = finfo{2}; data = read(nb, fullrawfile, 'yearbase', 2001, 'ilist', ilist,... 'use_ext_heading', 1, 'vars', 'all') aux_struct = get_serfields(data,'verbose',1,... 'gpspath', 'gbinfiles/pcode', 'adupath', 'gbinfiles/adu2',... 'hdgpath', 'gbinfiles/fyro', 'spdpath', 'gbinfiles/sndspd') data = update_raw(data, aux_struct); data.depth = mk_depth(data, 5); OH = 45.0 + .55; %Mounting Angle + phase hdg = data.heading; [data.enu data.xyze] = beam_enu(data.vel, OH + hdg, 0*hdg, 0*hdg', ... 'geometry','convex'); [dd, nbconfig] = restruct(nb, data); ###----------- [dd,config] = get_rndata(94 + [0 5*300/86400], 'gbinfiles'); rlookit(dd, config, 1, [15]) rlookit2(dd, config, [15]) ============================================================================= params.h_align = 45 + .55; params.h_bias = 0; params.ilayer = [2:20]; params.interval = 300; params.geometry = 'concave'; params.yearbase = 2001; params.add_to_depth = 5; instclass = nb; rawadcppath = '../raw/adcp_pings'; files = dirs(fullfile(rawadcppath, '*.raw'), 'fullpath', 1); adcppath r = []; for ifile = 1:length(files) file = files(ifile).name; r = load_raw(instclass, file, params, 'finish', 0, 'leftover', r, ... 'use_external_gyro', 1); end