.. index:: ! mgd77sniffer .. include:: ../module_supplements_purpose.rst_ ************** mgd77sniffer ************** |mgd77sniffer_purpose| Synopsis -------- .. include:: ../../common_SYN_OPTs.rst_ **gmt mgd77sniffer** *GEODAS-ids* [ |-A|\ *fieldabbrev*,\ *scale*,\ *offset* ] [ |-C|\ *maxspd* ] [ |-D|\ **d**\|\ **e**\|\ **E**\|\ **f**\|\ **l**\|\ **m**\|\ **s**\|\ **v**\ [**r**] ] [ |-E| ] [ |-G|\ *fieldabbrev*,\ *imggrid*,\ *scale*,\ *mode* or |-G|\ *fieldabbrev*,\ *grid* ] [ |-H| ] [ |-I|\ *fieldabbrev*,\ *rec1*,\ *recN* ] [ |-L|\ *custom-limits-file* ] [ |-M| ] [ |-N| ] [ |SYN_OPT-R| ] [ |-S|\ **d**\|\ **s**\|\ **t** ] [ |-T|\ *gap* ] [ |SYN_OPT-V| ] [ |-W|\ **c**\|\ **g**\|\ **o**\|\ **s**\|\ **t**\|\ **v**\|\ **x** ] [ |-Z|\ *level* ] [ |SYN_OPT-bo| ] [ |SYN_OPT-do| ] [ |SYN_OPT-n| ] [ |SYN_OPT--| ] |No-spaces| Description ----------- **mgd77sniffer** scans old (pre-Y2K) and new format ASCII MGD77 files for errors using point-by-point sanity checking, along-track detection of excessive slopes, and optional comparison of cruise data with global gravity and predicted bathymetry grids. Detected data problems are output by default as verbose descriptions of each detected error, often resulting in multiple messages per scanned record. Data problems are optionally output (**-De** option) using a computer-parseable format (see E77 ERROR FORMAT description below). Default error thresholds are derived from histograms of all MGD77 geophysical data collected between 1952 and January, 2006. Thresholds are adjustable with the |-L| option. Grids for comparison with cruise data may be downloaded via the web. Required Arguments ------------------ .. include:: explain_ncid.rst_ Optional Arguments ------------------ .. _-A: **-A**\ *fieldabbrev*,\ *scale*,\ *offset* Apply scale factor and offset adjustment to specified data field. Allows adjustment of cruise data prior to along-track analysis. CAUTION: data must be thoroughly examined before applying these global data adjustments. May not be used for multiple cruises. .. _-C: **-C**\ *maxspd* Set maximum ship speed in m/s, or knots with |-N| option. Ship speeds exceeding 10 m/s (~20 knots) are flagged as excessive by default. .. _-D: **-D**\ **d**\|\ **e**\|\ **E**\|\ **f**\|\ **l**\|\ **m**\|\ **s**\|\ **v**\ [**r**] Suppress default warning output and only dump cruise data row-by-row such as values, gradients, grid-cruise differences, E77 error summaries for each record, re-created MGD77 records or sniffer limits. Append **r** to include all records (default omits records where navigation errors were detected). **-Dd** output differences between cruise and grid data. Requires |-G| option. Output columns include: *lat lon dist cruiseZ gridZ diff [cruiseZ2 gridZ2 diff2 ...]* **Note**: Grid values are subtracted from cruise data so a positive difference implies cruise > grid. For multiple grid comparison, *cruiseZ gridZ diff* are repeated for each grid comparison in command line order. **-De** output E77 error classification format. Error output is divided into (1) a header containing information globally applicable to the cruise and (2) individual error records summarizing all errors encountered in each cruise record. mgd77sniffer writes E77 directly to file handle. See **E77 ERROR FORMAT** below for additional details. **-DE** Same as **-De** but no regression tests will be carried out. **-Df** output delta Z (change in geophysical field) column and delta S (change in distance) for each geophysical field. Distance between observations often differ for different fields depending on instrument sampling rate, so ds is included for each geophysical observation. Output columns include: *d[twt] ds d[depth] ds d[mtf1] ds d[mtf2] ds d[mag] ds d[diur] ds d[msd] ds d[gobs] ds d[eot] ds d[faa] ds* **-Dl** display mgd77sniffer limits. Customize this output to create a custom limits file for the |-L| option. No additional arguments are required. Output columns include: *fieldabbrev min max maxSlope maxArea* **-Dm** output MGD77 format records in Y2K-compliant MGD77 format **-Dn** output distance to coast for each record. Requires the **-Gnav** option. Output columns include: *lat lon dist distToCoast* **-Ds** output calculated gradients for speed and geophysical fields. Gradients correspond to the gradient type selected in the |-S| option (spatial derivatives by default). Output columns include: *speed d[twt] d[depth] d[mtf1] d[mtf2] d[mag] d[diur] d[msd] d[gobs] d[eot] d[faa]* See **MGD77 FIELD INFO** below for field and abbreviations descriptions. **-Dv** display values for the twelve position and geophysical fields for each MGD77 data record (in this order): *lat lon twt depth mtf1 mtf2 mag diur msens gobs eot faa* See below for **MGD77 FIELD INFO**. .. _-E: **-E** Reverse navigation quality flags (good to bad and vice versa). May be necessary when a majority of navigation fixes are erroneously flagged bad, which can happen when a cruise's first navigation fix is extremely erroneous. Caution! This will affect sniffer output and should only be attempted after careful manual navigation review. .. _-G: **-G**\ *information* Compare cruise data to GMT or IMG grids. Use one of the formats below. **-G**\ *fieldabbrev*,\ *imggrid*,\ *scale*,\ *mode* Compare cruise data to the specified grid in Sandwell/Smith Mercator format. Requires a valid MGD77 field abbreviation (see **MGD77 FIELD INFO** below) followed by a comma, the path (if not in current directory) and grid filename, a scale to multiply the data (1 or 0.1), and mode which stand for the following: (0) Img files with no constraint code, returns data at all points, (1) Img file with constraints coded, return data at all points, (2) Img file with constraints coded, return data only at constrained points and NaN elsewhere, and (3) Img file with constraints coded, return 1 at constraints and 0 elsewhere. **-G**\ *fieldabbrev*,\ *grid* Compare cruise data to the specified grid. Requires a valid MGD77 field abbreviation (see **MGD77 FIELD INFO** below) followed by a comma, then the path (if not in current directory) and grid filename. Multiple grid comparison is supported by using separate |-G| calls for each grid. See **GRID FILE INFO** below. Grid comparison activates several additional error checks. (1) Re-weighted Least Squares Regression of ship versus grid data determines slope and intercept shift, which when differing from expected 1 and 0, respectively, may indicate incorrectly scaled ship data, including incorrect units or instrument drift as well as erroneous gravity tie-in. (2) Accumulated ship grid offsets are computed along-track and excessive offsets are flagged according to *maxArea* threshold (use |-L| option to adjust *maxArea*). Warning: predicted bathymetry grids are constrained by cruise data so grids and cruise data are not always independent. Comparison of cruise bathymetry with predicted bathymetry grids also activates a "navigation crossing over land" check. .. _-H: **-H** (with **-G**\|\ **g** only) disable (or force) decimation during RLS analysis of ship and gridded data. By default mgd77sniffer analyses both the full and decimated data sets then reports RLS statistics for the higher correlation regression. **-Hb** analyze both (default), report better of two. **-Hd** to disable data decimation (equivalent to -H with no argument). **-Hf** to force data decimation. .. _-I: **-I**\ *fieldabbrev*,\ *rec1*,\ *recN* Append a field abbreviation and the first and last record in a range of records that should be flagged as bad (and set to NaN prior to the analysis). Repeat as many times as needed. May not be used for multiple cruises. .. _-L: **-L**\ *custom-limits-file* Override mgd77sniffer default error detection limits. Supply path and filename to the custom limits file. Rows not beginning with a valid MGD77 field abbreviation are ignored. Field abbreviations are listed below in exact form under MGD77 FIELD INFO. Multiple field limits may be modified using one default file, one field per line. Field min, max, max slope and max area may be changed for each field. Max slope pertains to the gradient type selected using the |-S| option. Max area is used by the |-G| option as the threshold for flagging excessive offsets from the specified grid. Dump defaults **-Dl** to view syntax or to quickly create an editable custom limits file. Example custom default file contents (see below for units): +--------------+--------+---------+------------+-----------+ | # abbrev | min | max | maxSlope | maxArea | +--------------+--------+---------+------------+-----------+ | twt | 0 | 15 | 1 | 0 | +--------------+--------+---------+------------+-----------+ | depth | 0 | 11000 | 500 | 5000 | +--------------+--------+---------+------------+-----------+ | mag | -800 | 800 | -- | -- | +--------------+--------+---------+------------+-----------+ | faa | -300 | 300 | 100 | 2500 | +--------------+--------+---------+------------+-----------+ Use a dash '-' to retain a default limit. Hint: to test your custom limits, try: mgd77sniffer **-Dl** **-L**\ .. _-M: **-M** Adjust navigation on land threshold (meters inland) [100]. .. _-N: **-N** Use nautical units. .. _-R: .. |Add_-Rgeo| unicode:: 0x20 .. just an invisible code .. include:: ../../explain_-Rgeo.rst_ .. _-S: **-S**\ **d**\|\ **s**\|\ **t** Specify gradient type for along-track excessive slope checking. **-Sd** Calculate change in z values along track (dz). Output is given in geophysical units, e.g., mGal. **-Ss** Calculate spatial gradients (dz/ds). Output is given in geophysical units per km along the survey track, e.g., mGal/km. **-St** Calculate time gradients (dz/dt) [default]. Output is given in geophysical units per second along the survey track, e.g., mGal/sec. .. _-T: **-T**\ *gap* Adjusts mgd77sniffer gap handling. By default, data gaps greater than 5 km are skipped. Set to zero to de-activate gap skipping. .. _-W: **-W**\ **c**\|\ **g**\|\ **o**\|\ **s**\|\ **t**\|\ **v**\|\ **x** Print out only certain warning types for verbose error messages. Comma delimit any combination of **c\|g\|o\|s\|t\|v\|x**: where (**c**) type code warnings, (**g**)radient out of range, (**o**)ffsets from grid (requires **-G**\|\ **g**), (**s**)peed out of range, (**t**)ime warnings, (**v**)alue out of range, (**x**) warning summaries. By default ALL warning messages are printed.Not compatible with any |-D| options. .. |Add_-V| replace:: |Add_-V_links| .. include:: /explain_-V.rst_ :start-after: **Syntax** :end-before: **Description** .. _-Z: **-Z** Flag regression statistics that are outside the specified confidence level. (i.e., **-Z**\ 5 flags coefficients m, b, rms, and r that fall outside 95%.) .. |Add_-bo| replace:: Output binary data for **-D**\ d\|f\|s\|v option. .. include:: ../../explain_-bo.rst_ .. |Add_-do| unicode:: 0x20 .. just an invisible code .. include:: ../../explain_-do.rst_ .. include:: ../../explain_-n.rst_ .. include:: ../../explain_help.rst_ .. include:: ../../explain_grdresample2.rst_ Mgd77 Field Info ---------------- +-------------+------------------+-------------+ | *Field* | *Abbreviation* | *Units* | +-------------+------------------+-------------+ | Two-way | Travel | Time | +-------------+------------------+-------------+ | Corrected | Depth | depth | +-------------+------------------+-------------+ | Mag | Total | Field1 | +-------------+------------------+-------------+ | Mag | Total | Field2 | +-------------+------------------+-------------+ | Residual | Magnetic | mag | +-------------+------------------+-------------+ | Diurnal | Correction | diur | +-------------+------------------+-------------+ | Mag | Sensor | Depth/Alt | +-------------+------------------+-------------+ | Observed | Gravity | gobs | +-------------+------------------+-------------+ | Eotvos | Correction | eot | +-------------+------------------+-------------+ | Free | Air | Anomaly | +-------------+------------------+-------------+ Grid File Info -------------- For |-G| the grids must either be in the img format used by Sandwell & Smith, which is a spherical Mercator 2-byte grid with no header, or any regular grid type supported by GMT. E77 Error Format ---------------- **Header** Information pertaining to an entire cruise, such as NCEI and survey institution identification codes, cruise examination time, two-way travel time corrector information, data precision warnings, as well as systematic scales, constant offsets and correlation coefficients from global grid comparisons are reported as E77 header information. **Sample** # Cruise 08010039 ID 74010908 MGD77 FILE VERSION: 19801230 N_RECS: 3066 # Examined: Wed Oct 3 16:30:13 2007 by mtchandl # Arguments: -De -Gdepth,/data/GRIDS/etopo5_hdr.i2 N Errata table verification status # mgd77manage applies corrections if the errata table is verified (toggle 'N' above to 'Y' after review) # For instructions on E77 format and usage, see `http://gmt.soest.hawaii.edu/mgd77/errata.php `_ # Verified by: # Comments: # Errata: Header Y-E-08010039-H13-02: Invalid Magnetics Sampling Rate: (99) [ ] Y-W-08010039-H13-10: Survey year (1975) outside magnetic reference field IGRF 1965 time range (1965-1970) Y-I-08010039-depth-00: RLS m: 1.00053 b: 0 rms: 127.851 r: 0.973422 significant: 1 decimation: 0 Y-W-08010039-twt-09: More recent bathymetry correction table available Y-W-08010039-mtf1-10: Integer precision Y-W-08010039-mag-10: Integer precision **Error Record** Individual error records have strict format. Included is a time or distance column followed by record number, a formatted error code string, and finally a verbose description of errors detected in the record. Three error classes are encoded into the error code string with different alphabetic characters representing unique error types. See below for error code format description. **Format**