Guy R. Cochrane
2005
SANAHAB -- Benthic Habitat polygons for South Anacapa Island (UTM 10N, NAD83)
(Volume II, Version 1.0, 2005)
vector digital data
Open-File Report
2005-1170
Pacific Coastal and Marine Science Center, Santa Cruz, CA
U.S. Geological Survey
http://pubs.usgs.gov/of/2005/1170/habitat/sanahab.tgz
http://pubs.usgs.gov/of/2005/1170/catalog.html
https://doi.org/10.3133/ofr20051170
Guy R. Cochrane
James E. Conrad
Jane A. Reid
Sarah Fangman
Nadine Golden
2005
Nearshore Benthic Habitat GIS for the Channel Islands National Marine Sanctuary and Southern California State Fisheries Reserves, Volume II Edition: 1.0
1.0
Open-File Report
2005-1170
Pacific Coastal and Marine Science Center, Santa Cruz, CA
U.S. Geological Survey
https://doi.org/10.3133/ofr20051170
Benthic habitat polygon coverages have been created for marine reserve locations surrounding the Santa Barbara Basin. Diver, ROV and submersible video transects, bathymetry data, sedimentary samples, and sonar mapping, have been integrated to describe the geological, biological, and oceanographic aspects of habitat. Anacapa Reserve, is part of the Marine Ecological Reserves Research Program (MERRP). The U.S. Geological Survey (USGS), in a cooperative project with Sea Grant-MERRP and investigators at National Marine Fisheries Service (NMFS), the Channel Islands National Marine Sanctuary (CINMS), and National Park Service (NPS) has collected sidescan sonar and video data to produce a polygon coverage. The habitat polygons have attributes for megahabitat, bottom induration, macrohabitat (where macrohabitat observations are available), polygon area, polygon perimeter, and water depth. The habitat GIS shows rocky habitat suitable for rockfish (Sebastes sp.), abalone (Haliotis sp.), and other threatened benthic species from the shoreline out to the 100-m depth limit of the survey.
These data are intended for science researchers, students, policy makers, and the general public. The data can be used with geographic information systems (GIS) software to display geologic and oceanographic information.
Additional information about the field activities from which this data set was derived are available online at http://walrus.wr.usgs.gov/nearshorehab/
19990301
20000718
ground condition
As needed
-119.456723
-119.331627
34.027738
33.981107
USGS Metadata Identifier
USGS:59f73c10-e5b1-426c-b6a0-790825baf92e
USGS Thesaurus
scientific interpretation
sea-floor characteristics
habitats
geology
marine geology
None
U.S. Geological Survey
USGS
Coastal and Marine Hazards and Resources Program
CMHRP
Pacific Coastal and Marine Science Center
PCMSC
Coastal Geology
benthic habitat
fisheries
seafloor
ISO 19115 Topic Category
oceans
biota
geoscientificinformation
None
South Anacapa Island
Channel Islands
Channel Islands National Marine Sanctuary
Southern California
Santa Cruz Islands
Santa Barbara
Ventura
California
CA
North Pacific Ocean
Northern Pacific Ocean
United States
west coast
USA
None
USGS-authored or produced data and information are in the public domain from the U.S. Government and are freely redistributable with proper metadata and source attribution. Please recognize and acknowledge the U.S. Geological Survey as the originators of the dataset and in products derived from these data.
U.S. Geological Survey, Pacific Coastal and Marine Science Center
PCMSC Science Data Coordinator
mailing and physical
2885 Mission Street
Santa Cruz
CA
95060-5792
US
831-427-4747
pcmsc_data@usgs.gov
http://pubs.usgs.gov/of/2005/1170/images/sanahab.jpg
JPEG image of habitat polygons
JPEG
Thanks to the Staff of the Channel Islands National Marine Sanctuary, the crew of the NOAA R/V Ballena, the crew of the NOAA R/V MacArthur, and the crew of the UCSD R/V Sproul.
SunOS, 5.8, sun4u UNIX; ArcInfo version 8.0.2
Habitat polygons dervived in ArcGIS 9.0 from a georefereced sidescan sonar mosaic tiff
Habitat attribute types are from Greene, G.H., Yoklavich, M.M., Starr, R.M., O'Connell, V.M., Wakefield, W.W., Sullivan, D.E., McRea, J.E., and Cailliet, G.M., 1999. A classification scheme for deep seafloor habitats. Oceanologica Acta, 22, 663-678.
Macrohabitat attributes assignments are limited to areas where bottom video has been collected.
Polygon topology present. Every polygon has a label and are all polygons
closed
Macrohabitat classification is missing where video information is lacking
Accuracy of the horizontal coordinates is on the order of 10 m based on uncertainty in position of sidescansonar fish relative to ships gps position.
>--------clip the image mosaic----------------------------
starting with 1m resolution mosaic sonar image sana1m.img (see proceesing history for development of mosaic) on rouse
convert to sana1m.tif with export
ftp to desktop
imagegrid sana1m.tif sana1mg
use arcedit to find xy extent of valid pixels
gridclip sana1mg sana1mgc x1 y1 x2 y2
del sana1m.tif sana1m.tfw
gridimage sana1mgc none sana1m.tif tiff none
on rouse rm sana1m.tif sana1m.img sana1m.lbl
import sana1m.tif sana1m.img
>---------classification of rock areas----------------
csh rockjob1 for eastern area
csh rockjob2 to classify rock in western anacapa passage area
mask and mosaic together to produce sana1mrck_msk.img
stretch 0;0 1;255 20;255 21;0 254;0 255;255 to produce sana1mrck4.img
ftp to desktop for photoshop editing
open in photoshop and duplicate layer on sana1m.raw as background
photoshop painting out noise with black
>----------classification of mixed areas-------------
on rouse:
csh mixedjob
sana1mmix.img rename sana1mmix.raw
ftp to desktop
open in photoshop and duplicate layer on sana1m.raw as background, then save as sana1mmix1.psd
photoshop painting out noise with black
save as sana1mmix1.raw
ftp to rouse
convert to tiff sana1mmix1.tif with export
ftp to desktop
imagegrid sana1mmix1g
gridpoly sana1mmix1p
arcedit sana1mmix1p
sel area < 10 and grid-code = 0
calc grid-code = 255
polygrid sana1mmix1p sana1mmix2g grid-code
gridpoly sana1mmix2g sana1mmix2p
>------------------------------------
Nadine Golden starts editing the data at this point
arcedit to remove zero polygons that are shadow
save sana1mmix3p
polygrid sana1mmix3p sana1mmix4g
gridpoly sana1mmix4g sana1mmix4p
arcedit to remove 0 gridcode polygons in mixed areas at east and west
edge of the mosaic
save sana1mmix4p
polygrid sana1mmix4p sana1mmix5g
ae
sel grid-code = 255
calc grid-code = 170
polygrid sana1mmix3p sana1mmix4 grid-code
>------------------------------------
for soft bottom
stretch sana1m sana1mmud 0;0 1;85 255;85
export sana1mmud.tif
imagegrid sana1mmud.tif sana1mmud
>---------------------------------------------------
//converted tiff to grid in arcinfo using imagegrid command
imagegrid sana1mmud sana1mmud1g
imagegrid sana1mrck12 sana1mrck12g
//cleaned out Photoshop values by converting grid to polygon and edited polygon in arcinfo.
gridpoly sana1mrck12g sana1mrck12p
ae
ec sana1mrck12p
sel grid-code = 255 or grid-code = o
nselect
calc grid-code = 0
polygrid sana1mrck12p sana1mrck13g grid-code
//merged grids in arcinfo
copy sana1mmud1g sana1hab1g
grid
gridedit edit sana1hab1g
gridedit gridmerge zero sana1mmix5g sana1mrck13g
//Steps for creating anacapa island grid
1. created polygon feature class of anacapa island in ArcMap by tracing the island off the coast shape file using the edit mode trace tool.
anacapa_island.shp
2. Converted polygon feature class to polygon coverage
using ArcMap Spatial Analyst-->convert polygon feature to polygon coverage.
anacapa_island.shp-->anacapap1
3. cleaned coverage using ArcInfo
build anacapaP1
clean anacapaP1
4. converted polygon coverage to grid using ArcInfo poly grid anacapap1 anacapag1 grid-code
//Steps to creating near shore rock grid (using ArcMap and ArcTool Box)
1. created polygon feature class of rock in ArcMap by loosely tracing the outer (closest to land) rock area and closing the polygon with a line.
rock.shp
2. created grid using arctoolbox feature class to grid toolrock.shp rockg1
3. using spatial analyst tool reclassify, converted values of rockg1 from 0 to 255 and named new file: rock2g
//Calculate final grid with cleaned near shore data (from mud to rock) and no data where there is land
1. Set up ArcMap project with all grids: sana1mhab2g, anacapag1, rock2g
2. Spatial Analyst tool
-set option to Extent-->union of inputs.
-in raster calculator dialogue box merge grids of rck and hab:
sana1mhab3g = merge([rock2g],[san1mhab2g])
//Calculate no data where there is land
1. Create shapefile mask
-create new polygon feature class in ArcCatlog
-add new polygon to project
-using ArcMap Editor make new polygon a rectangle around all data (around sana1mhab3g)
-in arctoolbox-->analysis tool-->-->erase
erase anacapa polygon from new rectangle polygon
new shapefile_erase has hole of island data
-in spatial analyst-->options-->set mask-->use drop down to select newerase shapefile
2. Recalculate sana1hab3g with new mask poly by using the spatial analyst's raster calculator
[sana1mhab4g] = [sana1mhab3g] --> select evaluate
resulting grid has a hole (no data) where land was
//set all 0 data to no data
1. in spatial analyst raster calculator divide grid by itself
sana1mhab4g]/[sana1mhab4g]
where 0/0 will equal no data
all other data will be equal to 1
calculation leaves you with value 1 where there was data
2. in spatial analyst raster calculator multiply new calculation by original grid:
sana1mhab5g = [sana1mhab4g] * [Calculation]
so all values * 1 gives you original data
//Breakup large mud polygon
1. Used Raster Cleanup tool to paint breaklines in polygon
2. converted to polygione shapefile.
Note: this step took several attempts in order to maintain integrity of data and the final shapefile in this step was sana1mhab21s.
3. edited polygon shapefile sana1mhab21s to asign new gridcodes to polygons in the west and north west region of data.
2. converted shapefile back to raster with Toolbox. final grid is sana1mhab21g.
//Filter grid to decrease polygon total
steps:
1. filtered original grid using the "low" filter default
filter sana1mhab21g sana1mhab23g
(note: made and error on grid sana1mhab22g so advanced one to 23g)
2. reclassified new grid using the categories you sent me in attached remap.txt file.
used spatial anlysis reclassification option
3. converted new floating point grid to an integer grid.
sana1mhab24g = int(sana1mhab23g)
4. Using Toolbox Raster to Features: converted new floating integer grid to polygon shapefile
new polygon shapefile: 169,051 polygons
original polygon shapefile: 386,777 polygons
20041215
Edited metadata to add keywords section with USGS persistent identifier as theme keyword. No data were changed.
20201019
U.S. Geological Survey
VeeAnn A. Cross
Marine Geologist
Mailing and Physical
384 Woods Hole Road
Woods Hole
MA
02543-1598
508-548-8700 x2251
508-457-2310
vatnipp@usgs.gov
Edited metadata to add USGS Thesaurus keywords and perform minor edits to bring the metadata up to current PCMSC standards. No data were changed. The metadata available from a harvester may supersede metadata bundled within a download file. Users are advised to compare the metadata dates to determine which metadata file is most recent.
20211021
U.S. Geological Survey
Susan Cochran
Geologist
Mailing and Physical
2885 Mission Street
Santa Cruz
CA
95060
831-460-7545
scochran@usgs.gov
Vector
G-polygon
67875
Universal Transverse Mercator
10
0.999600
-123.000000
0.000000
500000.000000
0.000000
coordinate pair
.000016
.000016
meters
North American Datum of 1983
Geodetic ReferenceSystem 80
6378137
298.2572222
>
>sanahab Fields:
>
>NAME ALIAS TYPE LENGTH PRECISION SCALE NUMBER_FORMAT
>ID ID Double 10 10 0 Numeric
>GRIDCODE GRIDCODE Double 10 10 0 Numeric
>CODE CODE String 10 10 0 -
>MEGA_ID MEGA_ID String 5 0 0 -
>MSO_MRC_ID MSO_MRC_ID String 5 0 0 -
>MDFR_ID MDFR_ID String 5 0 0 -
>BOTTOM_ID BOTTOM_ID String 5 0 0 -
>GEO_UNIT GEO_UNIT String 50 0 0 -
>Area Area Double 19 18 11 Numeric
Benthic habitat classification attributes: megahabitat, bottom induration, meso-macrohabitat, and modifiers from Green and others, 1999.
CODE is a combination of the habitat attributes.
MEGA_ID is usually S for Shelf, but may be F for basin or canyon flank.
BOTTOM_ID is h for hard bottom, m for mixed hard and soft bottom, or s for soft sediment bottom
MSO_MRC_ID are visual observations when sand waves (w) were observed. These macrohabitats described in Greene and others 1999.
MDFR_ID are modifiers to describe the texture or lithology of the seafloor and appear in the code preceded by an underscore (_). Including; fractured (_f), differently eroded (_d), kelp (_k), and limestone (_l)
Habitat attribute types are Modified after Greene, G.H., Yoklavich, M.M., Starr, R.M., O'Connell, V.M., Wakefield, W.W., Sullivan, D.E., McRea, J.E., and Cailliet, G.M., 1999. A classification scheme for deep seafloor habitats. Oceanologica Acta, 22, 663-678.
Guy R. Cochrane
U.S. Geological Survey
Geophysicist
mailing and physical address
2885 Mission Street
Santa Cruz
CA
95060-5792
USA
(831) 427-4754
(831) 427-4748
gcochrane@usgs.gov
Downloadable Data
Although these data have been used by the U.S. Geological Survey (USGS), U.S. Department of the Interior (DOI), no warranty expressed or implied is made by the U.S. Geological Survey as to the accuracy of the data. The act of distribution shall not constitute any such warranty, and no responsibility is assumed by the USGS in the use of these data or related materials.
Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
shapefile
3.3
ESRI Shapefile Format
The SHP file contains the geospatial data. The SHX file contains the index of the geospatial data. The DBF file contains the attribute data in dBase format. The PRJ file contains the coordinate system information (optional). The AVL file contains the legend information (optional). The SBN and SBX files contain the spatial index of the geospatial data (optional). The XML file contains the metadata describing the data set <data set name>.shp.xml. An ASCII version of the metadata file. A browse graphic showing the data layer coverage and extent (optional).
zip archive
35.2
http://pubs.usgs.gov/of/2005/1170/habitat/sanahab.tgz
http://pubs.usgs.gov/of/2005/1170/catalog.html
https://doi.org/10.3133/ofr20051170
Data may be retrieved via any WWW browser.
None
These data are available in Environmental Systems Research Institute (ESRI) shapefile format. The user must have ArcGIS or ArcView 3.0 or greater software to read and process the data file. In lieu of ArcView or ArcGIS, the user may utilize another GIS application package capable of the importing data. A free data viewer, arcexplorer, capable of displaying the data is available from ESRI at www.esri.com.
20211021
U.S. Geological Survey, Pacific Coastal and Marine Science Center
PCMSC Science Data Coordinator
mailing and physical
2885 Mission Street
Santa Cruz
CA
95060-5792
US
831-427-4747
pcmsc_data@usgs.gov
Content Standard for Digital Geospatial Metadata
FGDC-STD-001-1998
local time