Hi John-
Thanks for the helpful reply!
I'm going to intersperse some more questions/comments into your
instructions, since additional clarification may eventually help others.
On 09/06/2012 05:33 PM, John Caron wrote:
Hi Ellyn:
On 8/21/2012 8:35 AM, Ellyn Montgomery wrote:
Folks-
I'm trying to verify that an aggregation has done what I expect using
toolsUI, and am having some trouble.
Putting my ncml file in the ncml aggregation window produces reasonable
looking file structure. Then if I put the same ncml in the viewer it
looks reasonable too, but do I expect to ever see values if I click on a
variable? A mouse-over on the variable shows the attributes, but I
never see the data in the variable, despite clicking.
in the viewer tab, select variable, right click and choose "ncdump
data". that takes you to a "ncdump variable data" popup window, with
the full extent of the variable in the
Here's what I see after selecting a dataset and (left) clicking on
salinity in either the left or right pane, then right clicking salinity
in the *right *pane (under description) :
for example, i changed to:
S_40(0:105483:1000, 0:0:1, 0:0:1, 0:0:1)
How did you modify S_40 to limit the display? In the above, my only
option is to click NCdump, and everything gets listed in the little
NCdump box.
to keep the output low.
this was working for me.
The above is really good to know because I was expecting the data to be
displayed in the grey area under the last variable name as happens in
some of the other tabs.
I also tried
opening it in the FeatureTypes tab, and had similar results. Perhaps
there isn't a way to display a variable's content in toolsUI? The ncml
is attached, if you want to try for yourselves.
Also, in toolsUI4.2 (webstart), I am able to create a netcdf file from
the ncml without errors, though when checked in Matlab, the variable
content is not what I expect (coordinate vars are OK, but not the
others). When I downloaded the new v4.3 toolsUI and used it to save as
netcdf, it displayed "error:null" during the file creation, and in this
case, the coordinate variables were good, and the others were all 0.
http://geoport.whoi.edu/thredds/dodsC/MBAY_LT/7551mc-a1h.nc is missing
the variable T_20. If you put the ncl file in the "Aggregation" tab,
then hit the "check files" buttom on upper right, you get a report
(see below). there are enough problems to suggest that this collection
of files is not suitable for a "joinExisting" aggregation, which
requires (almost) exact files except or the aggregation coordinate.
I think what you said is that although the aggregation I'm attempting
doesn't crash and burn, it's really failing because the files in the
joinExisting don't have the same content (variables). Best practice
should be to do "check files" first and ensure there aren't a lot of
errors about missing variables.
In theory then, if I removed the files with missing temperature, and
only aggregated on T_20 (leaving out all the other variables that may or
may not be present) it would work?
So if I want to aggregate temperature from files with variables called
T_20, T_24, T_28 (all with standard_name = sea_water_temperature), I'd
need to rename the variables in ncml, put that new catalog in TDS, then
aggregate from the new spot?
Or is doing a 2-part aggregation a better approach? step 1 might be
aggregating the three names for temperature separately (one for T_20,.
one for T_24, and one for T_28), renaming the output variable to the CF
name each time, then aggregate the 3 files to get one long temperature
record?
also:
1) the extra lat,lon dimension on the variables is actually incorrect.
however it "works" because its equal to 1,1.
We're in the process of re-doing the ncml to represent the data as
discrete samples, and the extra lat and lon dimensions will be removed
there. We kept our data as "grid" representation because in earlier CF
versions I couldn't get PointFeatures to handle the multiple depths in
adcp data correctly.
2) if you are running a TDS server >= 4.2, enabling the cdmremote
service and using it for remote aggregations like this will speed up
response time.
We'll try this.
Thanks again for the help!
Best, Ellyn
John
------------------------------
Original =
file:E:/work/ellyn/nrsfc_ts0812g.ncml#http://geoport.whoi.edu/thredds/dodsC/MBAY_LT/3391ats-a1h.nc
CompareTo=
file:E:/work/ellyn/nrsfc_ts0812g.ncml#http://geoport.whoi.edu/thredds/dodsC/MBAY_LT/3411sc-a1h.nc
T_20(time=2680, depth=1, lat=1, lon=1) != T_20(time=2496, depth=1,
lat=1, lon=1)
S_40(time=2680, depth=1, lat=1, lon=1) != S_40(time=2496, depth=1,
lat=1, lon=1)
MISSING 'ATTN_55' in 2nd file
MISSING 'C_50' in 1st file
MISSING 'STH_71' in 1st file
MISSING 'tran_4010' in 1st file
--------------------------------
Original =
file:E:/work/ellyn/nrsfc_ts0812g.ncml#http://geoport.whoi.edu/thredds/dodsC/MBAY_LT/3391ats-a1h.nc
CompareTo=
file:E:/work/ellyn/nrsfc_ts0812g.ncml#http://geoport.whoi.edu/thredds/dodsC/MBAY_LT/3481sc-a1h.nc
T_20(time=2680, depth=1, lat=1, lon=1) != T_20(time=2483, depth=1,
lat=1, lon=1)
S_40(time=2680, depth=1, lat=1, lon=1) != S_40(time=2483, depth=1,
lat=1, lon=1)
MISSING 'ATTN_55' in 2nd file
<rest of output snipped here>
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--
Ellyn T. Montgomery, Oceanographer and Data Manager
U.S. Geological Survey
Woods Hole Coastal and Marine Science Center
384 Woods Hole Road, Woods Hole, MA 02543-1598
(508)457-2356
