After feedback from DMW's first look at SEaPT, the file selection and loading routine was modified. Instead of opening a single file selection dialog, the entire csv dir is viewable, listing all sta.csvs in a scrollable listbox. Single-click the sta.csv to edit, select the desired columns, then press [Display Sel Cols]. To view the entire sta.csv, there is a [Display All Cols] button as well.
As per DMW's suggestion, Cruise, Ord_Occ, Niskin, Sample, and Depth are pre-selected by default but can be unselected if desired.

Fix: original sta.csv array stored in memory is updated to new values when [Save Edits] is pressed. So the onscreen values refresh to match the new file values.

CSVEditor renamed to SEaPT (Sta.csv Editor and Plotting Tool) development begins. First, the sta.csv editor will be designed and allow easier sta.csv editing. Selecting specific columns (but loading the entire array).
Q:\DECODR\SEaptB1.exe is available.
First beta of the sta.csv editor compiled. I am still working on fine-tuning it and adding features but I would like you to give it a try. Like DECODR, seaptB1.exe will make a backup of the original in the bak dir if you Save.

Some info:
1). the csv editor is not part of DECODR obviously so it can be used side-by-side with DECODR.

2). Right now it is a basic editor so any field on the screen can be edited by single-clicking the field, backspace or mousing over the value and replaced/edited. These changes do not stick unless you click the Save button.

3). The first screen that appears is the basic menu - reads the decodr.cfg and loads the same cruise & datapaths as DECODR. But you can navigate to any csv dir, just be sure it has a bak subdir.

4). You can select as many or few columns as you want then click Disply Sel Cols. Or you can jump right in and click Display All Cols.

5). If you double-click any cell in a datacode column, the datacode dialog will appear. Right now only O2 (ODC) datacodes are linked ie if you change ODC then OxSDC & OuMDC will change too. I need some clarification on what others may need to be linked. If you single-click the datacode, you can key-enter a single edit.

6). If saved, the new file should be properly column-formatted for 89 column sta.csvs (all post 1210 cruises).

7). Since csv editor uses decodr.cfg, I disabled csveditor's own cfg. We can decide if this is not flexible enough and I can reinstate it.

8). You can leave seapt.exe in the DECODR dir or move it into its own dir. It relies on C:\decodr\decodr.cfg for default datapaths but can open any sta.csv anywhere (it will change the datapath accordingly so it will break the bak feature if that subdir is not available).

To add:

The casts.csv editor is not working yet but will be simple.

Plotting features - some gTool capabilities will be added so we can customize the capabilities without Grant.

CCTG has decided to build our own bottle valves using General Oceanics (spigots) and Home Depot parts (plugs). Research support price quote was expensive and we can save about 50% using off-the-shelf parts. Once a jig is setup, it will be much easier to make replacement valves.

calcofi.com et al at Hostgator is upgrading to 5.x
http://support.hostgator.com/articles/cpanel/php-configuration-plugin

Two fixes:
Julian Day less than 100 was only one or two char - now padded to three "001 - 099"

Prodo array values were carrying over from one station to the next since the array holding those values was not reset - fixed.

Most sea-going data acquisition workstations are still running XP. O2, Salt, Chl, backup Nutrient are running XP. A new i3 microPC was bought to upgrade the O2 auto-titrator along with two USB to Serial A-D (NI USB-6009) adapters. DMW was able to get it operational. Monitor mounting plate is missing but hopefully in a sea-going bin.

DECODR feature addition - in DECODR1404.exe, under the Contouring tab, on the far right, I've added two contouring-related file creation buttons.
Instead of using marker files, the new [Build Base TXT] will use processed, non-bottle-corrected CTD upcast .asc files to generate the standard level csvs used to generate the standard level contouring base files.

Then the [Create Contour CSVs] module will take the new txt file generated by [Build Base TXT] and create horizontal contour csvs. Anomalies are calculated during this step so the last step is to run the [Horizontals] module to generate the base contour files - the old CODES "email" file option is now "CTD asc". This will improve the preliminary plots since they will display 1m average data instead of "instantaneous" (0.042 second) mrk measurements.

Wanting to be consistent with column labeling that matched the nutrient data files, CESL was outputting NH4. This causes a problem with GTool so the easiest fix is to have CESL output NH3 again. Done...

Generating a Data Report from an old ieh (eg 8203) 2014

1). Convert a terpled ieh from Unix to DOS using Ultraedit File/conversions

2). DECODR's contouring module can use the terpled ieh to create map csvs - [ IEH > csv]

3). Run Horizontals module and pick IEH from the Input Data selection box (right side). NOTE: there needs to be a "MAPS" subdir under the Q:\CODES\1982\8203\ main dir. I configured DECODR for 8203 just to make it easier to run/rerun the modules.

4). Pick your Blank File - 8203 is only lines 93 & 90 so pick that blanking file

5). Uncheck any data type that is not in the IEH - 8203 did not have Chlorophyll or Nitrate

6). If Surfer generates misdrawn maps, load the contour and post files into a good version of map manually, replacing the grid file under Properties then save as under a new filename.

Once the t.ieh was converted from Unix to Dos I was also able to run Addthox2 & DareH.exe on it under Virtual XP. 8203t.ieh did not have sigma-theta or O2 sat in the ieh. 8203ta.ieh is the addthox2'd version of 8203t.ieh; 8203TAA.RPT is the DareH.exe version of the Data Report with interpolated nutrients (PO4 & Sil only for 8203; only 125m depth values were interpolated).

CESL1404 now highlights all the DIC additional sample depths on the sample form.

Added CTD salinity comparison to salt printout
New prn file format circa April 2014:
P O R T A S A L I O D - C A L C O F I
Expedition: CalCOFI 1404SH
Ship: R/V Ocean Starr
Portasal: 60-654 bath temp: 21.008 operator: JRW
std batch: SUB1 k-15: 0.99157 Standard: P155 = 0.99981 air temp: 18.9
Draw Date: 2014 Apr 11 18:08 Run Date: 2014 Apr 12 13:50

sta cs nis cr(1) cr(2) avg cr salt CTDS Diff box sbot time BathT cf
047 02 0000 0.99157 0.99157 0.99157 34.6690 000 'SUBS' 13:00:23 21.008 2
047 02 0001 0.98235 0.98234 0.98235 34.3073 34.3078 -0.0006 003 '0001' 13:04:02 21.008 2
047 02 0002 0.98043 0.98043 0.98043 34.2322 34.2324 -0.0002 003 '0002' 13:07:32 21.008 2
047 02 0003 0.97893 0.97893 0.97893 34.1735 34.1752 -0.0017 003 '0003' 13:09:58 21.008 2
047 02 0004 0.97793 0.97793 0.97793 34.1344 34.1357 -0.0013 003 '0004' 13:12:22 21.008 2
047 02 0005 0.97734 0.97734 0.97734 34.1113 34.1133 -0.0020 003 '0005' 13:14:47 21.008 2
047 02 0006 0.97655 0.97655 0.97655 34.0803 34.0812 -0.0009 003 '0006' 13:17:09 21.008 2
047 02 0007 0.97593 0.97593 0.97593 34.0561 34.0576 -0.0015 003 '0007' 13:19:17 21.008 2

Replacing the old format which had a lot of unused space:
P O R T A S A L I O D - C A L C O F I
Expedition: CalCOFI 1404SH
Ship: R/V Ocean Starr
Portasal: 60-654 bath temp: 21.009 operator: DMW
std batch: SUB1 k-15: 0.99157 Standard: P155 = 0.99981 air temp: 18.7
Draw Date: 2014 Apr 06 12:40 Run Date: 2014 Apr 07 07:25

sta cs nis cr(1) cr(2) avg cr salt box sbot time BathT cf
023 02 0000 0.99157 <1> 0.99157 <2> 0.99157 <2> 34.6690 000 'SUBS' 07:24:36 21.009 2
023 02 0001 0.98172 <1> 0.98172 <2> 0.98172 <2> 34.2828 003 '0001' 07:27:10 21.009 2
023 02 0002 0.98090 <1> 0.98091 <2> 0.98091 <2> 34.2509 003 '0002' 07:28:57 21.009 2
023 02 0003 0.98033 <1> 0.98034 <2> 0.98034 <2> 34.2285 003 '0003' 07:30:37 21.009 2
023 02 0004 0.97861 <1> 0.97862 <2> 0.97862 <2> 34.1612 003 '0004' 07:32:34 21.009 2
023 02 0005 0.97756 <1> 0.97755 <2> 0.97756 <2> 34.1197 003 '0005' 07:34:08 21.009 2...

Fixes - [CTD data to sta.csv] module adds both primary & secondary CTD data to all duplicate depths.

I changed CESL to make Mistrips recind 5 - there was a note in the code I wrote in 1212 that said it was changed because of terple issues. I think I have terple working on all recind except 9 right now but we should verify that.
Regarding ODC - are there CTD O2s to use in the station csv? If the CTD O2 data are missing, then the ODC will not be set to 1 or 2. So you may need to populate the CTD data fields for the update csvs datacoding to work properly. I will make the ODC blank when recind is 6 and ODC = 1 when recind is 5 but Ox1 has to have a value.

Since there may be some usefulness in keeping the ability of auto-datacoding-4 non-zero, deep, offshore ammonia, it is now an option. Next to the NH4 parameters of the nutrient module there is a checkbox labeled "4". If checked, it will datacode 4 non-zero deep offshore ammonia on whichever stations (> 60) are selected - you can run an individual station or subset of stations with this option toggled.

It should be noted that this option only affects the sta.csvs when the update sta.csv box is selected. Also, if the 4 box is unchecked, it will change previously datacoded 4 ammonias back to datacode 0 (but only offshore, non-zero, deep ammonias). Let me know if this is not desired and I can make it keep whatever datacode is present.

Fixes: calculates OxSatB using CTD salts if datacoded - useful for northern stations without all salts. Also eliminated odd ISL calculated salt at 1st ISL (~500m) if there are no salts to generate ISLs.

Fixes - handles stations numbering over 80 in the data modules (double-check and let me know if you see any weirdness).
Database-friendly csv generating routines have been embellished:
Cast columns in the bottle csv are now optional, checkbox toggled; "9"s are added to quality code columns of missing values.

Another glitch fixed - the dynamic height calculation routine was "blanking" the terpled bottle data. It was a misplaced $.

Prodos issues (can't remember the specifics - no email must have been a verbal communication) but it was fixed.

Problem 2: using the data code checker and there are no nuts run, like for all of the LTER bottles, decodr is putting a "4" in the datacode for NH4 where it should be a "9". The NDC is getting the proper "9" data code. Fixed.

I finally got around to adding that NH4 tabulation file to DECODR. I could not figure out a way to do it independent of the "update sta.csvs" option. So DECODR1312a will generate a tabulation file of NH4 values 'offshore & 200m or greater' or negative that are datacoded 4 or zeroed. Run the nutrient data processing routine, select update sta.csvs and it will generate a 1311NH4DC4.csv in the Nut dir.
If the '0 -' (zero negative values) box is checked, it will tabulate those as well but they will be datacoded '0'.
Be aware that this file will not be overwritten if already present. It will be appended so if you want to regenerate a fresh version, you will have to manually delete the 1311NH4DC4.csv.

Fixes & new features: missing dynamic height calculations have been addressed; ISL bottle density are no longer duplicates of CTD1 - uses terpled bottle salt value instead of CTD salt 1; NH4 negative value reporting is an option, as well as positive values offshore & below 200m. Both negative NH4 and deep-offshore positive NH4 values will have datacode 4 regardless. ISL NH4 adjacent to datacode 4 NH4s will also be zeroed.

Fixed the duplicate bottle dynamic height calculation.

I tweaked DECODR1312 a bit to handle some extraneous lines in the prd files & scin.csv. It worked fine using the 'box' values for 14C and blank (10.239 & 100), generating both an out file and updated sta.csvs. Be sure you check all the necessary boxes and use 1311scinR1.csv.

Changes to DECODR -
*added Nutrient feature: option to use RMNS or NH4 Check standard value for NH4.
*85 processing numbers hardwired into the Process form ie automatic file selection form where station files are pre-checked.
*Prodo routine tweaked to handle blank lines in prd### & YYMMscin.csv files.
*The latest DECODR1312 should calculate DynHt in either CTD to CSV module or the Derive Bottle Data module.

CalCOFI 1311NH: brand new WET Labs ECO-AFL/FL, replacing our Seapoint Fluorometer. Sensitivity
setting was 0-50mg/m^3. Seapoint is still operational and will become our primary backup.

Oxygens in umol/Kg: Derive umol/Kg routines improved in all related modules: Process Oxygens, CTD to CSV, Derive Bottle Data, Derive CTD Data. All umol/Kg oxygens are derived from ml/L using Seabirds algorithm:
oxyum! = (oxy * 44660) / (sigma + 1000)

Running the [Derive Bottle Data] & [Derive CTD Data] will work on t.csvs, preserving point-check datacodes. These routines will add umol/Kg values and other derived values in either the bottle or CTD cols. BE AWARE - if you derive/rederive t.csv file values and not sta.csvs file values, the files may be different so use cautiously.

umol/kg datacodes are the same as bottle oxygen ml/L datacodes since it is derived from that value.
Column labels in data products were updated to µmol/Kg & µM where appropriate, particularly in the Data Reports.

Tweaks to DICs: Reordered the DIC database csv so importing into the database does not require rearranging or adding columns. If DIC filename has a space, you will now be prompted to fix it. Most in-house applications do not like filenames with spaces.
Two DICS modules moved to Database tab - create DIC database csv & create Dickson csv. [Create Dickson csv] searches all the selected sta.csvs and creates a single csv with all the DIC bottle sample data to give to Dickson's lab. [Create DIC Database csv] will combine station csvs with Dickson/Cervantes DIC+TA csv for importing into the database.

Fixed: Extra bottle (recind 6) derived data removed or not calculated.
Fixed: bottle csv to database will include 0m depths
Tweak: cast csv to database calculates distance for all stations, including SCCOOS'

I tinkered with the µM/kg routines so all the values, including ISLs, will be available. Right now, the µM/kg data codes are cloned from the ml/L oxygen data codes since I am converting ml/L to µM/kg. I am also using the CTD derived sigma-theta (bottle algorithm) to calculate the µM/kg CTD value ie it uses the cruise or station corrected CTD oxygen and sigma-theta to calculate the µM/kg. It does not use the µM/kg contained in the CTD.csvs.

Fixed: Dynamic Height calculating erroneously for extra bottles, recind 6; fix = no value
Fixed: Cast database csv is missing secchi value - fixed.
Fixed: Integrated 14C col was empty - fixed
Fixed: Wind_Spd is missing from cast to database csv - fixed

New feature: DIC database csv module. Merges Cervantes DIC csv (export the tabular portion of the Excel file to csv) with sta.csvs bottle depths with matching DIC bottles.

Tweak: Made the Cast to database and Bottle to database modules create csvs in the same format as CIFT so the Access import specs will work for either.

1). "Select New Files" from a new subdir should be working for Nuts, Salts, Chls, O2s, & Prodos. Be aware that the .out file will be in that subdir.

2). NO3 correction is working now - a comparison if statement was ill-written.
3). RUN banner corrected in the nutrient out file

New features, modules, & bug fixes:
Nutrient QC - the output file to includes both uncorrected and corrected concentrations; if the difference between the corrected and uncorrected concentration is less than the minimum detection limit (MDL), no correction is applies; corrections (including 0 "non-corrections") are tabulated at the bottom of each run results. If the import corrected nutrients option is checked, the corrected nutrient concentrations will be imported into the station.csvs. Ammonia will use the 'NH4 Check' concentration value, not the RMNS or '99' NH4 concentration to correct the ammonia. This concentration is also tabulated at the bottom of each run to keep track of the correction, if any, that is applied.
Bug fix: module was expecting nutrient files to be in the nut subdir - now the module will allow nutrients to be in a subdir under the nut subdir and still find the other files (sta.csvs & casts.csv)

Added a casts+sta.csv WHP export module to DECODR1309.exe under the CSV tab. This module will build WHP-formatted _hy1.csvs from SIO-CalCOFI casts.csv & sta.csvs. Will add nutrient data codes next - not currently present in the almost completed module. CTD WHP formatter is next.

20 - 30 Aug 2013 - new nutrient QC routines: when processing nutrients, the 'RMNS' & 'NH4 Check' concentrations are compared to standard values. The standard (or expected values) are preloaded from csv file YYMMnut.cof (default), or user-selected .cof file, or user-entered or edited into the form's fields.
The corrected concentration is calculated using the %difference between observed and expected concentrations. These values are tabulated in the .out file, replacing the unused 'peak height' columns. %differences are also tabulated at the bottom of the run output. If 'Apply correction' & 'Update sta.csvs' are checked, the sta.csvs nutrient values will be updated with corrected concentrations whenever the %correction is greater than the %criteria and MDL.
Backup files of the sta.csvs before the update are copied to the bak subdir.

Many tweaks and updates have been programmed into DECODR in the last few months.

20 March 2013 - Adding Sigma-theta and Oxygen saturation to the sta.csv-to-ieh export are optional - checkboxes. Also fixed C14B & dark columns for prodo data; indexed improperly so easy fix.
08 May 2013 - Oxygen data code set/reset to zero by default.
14 May 2013 - tweaked the sta.csv column routine to use 89 cols on cruise 1210 to present. Older cruises may have sta.csvs that are 82 or 84 cols since the sta.csv format has been evolving.
14 May 2013 - tweaked the derivation of certain parameters, such as OxSat, DynHt, sigma-theta, to use CTD data when bottle data are not available - an issue primarily with northern stations which may only have two salts (surface & terminal depths).
06 Aug 2013 - non-confirmations fixes implemented; nutrient updates were not working properly because of missing bottles from non-confirmations in CTD data processing.
12 Aug 2013 - dynamic height fixes implemented related to non-confirmation and data codes - some 0 values were calculated because of data code skips, dynht uses a depth array (next bottle) to calculate properly. Data code was creating a gap/skip so the routine checks for the 2nd next bottle now.
19 Aug 2013 - major update to the nutrient module - RMNS & Quality Cup csv tabulation files are created when processing nutrients. Expected nutrient concentrations for each nutrient type (ie standard values) are compared to RMNS and the % offset calculated.