Difference between revisions of "Document domain characteristics by Mimi Tzeng"
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<br/><b>Details on how to do this task:</b> [[Document domain characteristics]]<br/><br/> | <br/><b>Details on how to do this task:</b> [[Document domain characteristics]]<br/><br/> | ||
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| + | As I understand this task, we are to take all of the variables used in the project and find the corresponding variable names from the [http://csdms.colorado.edu/wiki/CSN_Searchable_List CSDMS list]. So to start, here are lists of all of my variables. I'm just going to directly copy-paste from my scripts (MOORprocess_all.m and MoorADCP.m) for starters. I imagine the publication-ready version of this will be in three columns: the "common" name of the variable as oceanographers would understand it, the name of the variable in my code, and the name of the variable in the CSDMS. | ||
| + | |||
| + | <pre> | ||
| + | YSI | ||
| + | <ul> | ||
| + | ctddepth{3} = YSI(:,6); | ||
| + | ctdsal{3} = YSI(:,7); | ||
| + | ctdtemp{3} = YSI(:,8); | ||
| + | ctdpress{3} = YSI(:,9); | ||
| + | %ctdpress{3}(1:length(ctdtimestamp{3})) = NaN; | ||
| + | ctdcond{3} = YSI(:,10); | ||
| + | ctdspcond{3} = YSI(:,11); | ||
| + | ctdoxy{3} = YSI(:,13); | ||
| + | ctdoxysat{3} = YSI(:,14); | ||
| + | %ctdchla{3} = YSI(:,?); | ||
| + | %ctdturb{3} = YSI(:,15); | ||
| + | ctdturb{3}(1:length(ctdtimestamp{3})) = NaN; % a kludge for nonexistent variables in an existing package | ||
| + | ctdtds{3} = YSI(:,15); | ||
| + | </ul> | ||
| + | |||
| + | CTDs | ||
| + | <ul> | ||
| + | ctdtemp{r} = CTD(:,1); | ||
| + | ctdcond{r} = CTD(:,2); | ||
| + | ctdpress{r} = CTD(:,3); | ||
| + | ctdsal{r} = CTD(:,4); | ||
| + | ctdsound{r} = CTD(:,5); | ||
| + | ctdjday = CTD(:,6); %coming in, jday is Jan 1 = Day 1 | ||
| + | ctddens{r} = CTD(:,8); | ||
| + | ctddepth{r} = CTD(:,9); | ||
| + | ctdspcond{r} = CTD(:,10); | ||
| + | </ul> | ||
| + | |||
| + | Thermistors | ||
| + | <ul> | ||
| + | tempT{r} = dataT(:,1); | ||
| + | pressT = dataT(:,2); | ||
| + | depthT = cnv(:,2); | ||
| + | </ul> | ||
| + | |||
| + | CTD cast | ||
| + | <ul> | ||
| + | depth=datablock(:,3); | ||
| + | sal=datablock(:,4); | ||
| + | temp=datablock(:,5); | ||
| + | dens=datablock(:,6); | ||
| + | press=datablock(:,7); | ||
| + | cond=datablock(:,8); | ||
| + | spcond=datablock(:,9); | ||
| + | oxy=datablock(:,10); | ||
| + | oxysat=datablock(:,11); | ||
| + | ph=datablock(:,12); | ||
| + | chla=datablock(:,13); | ||
| + | par=datablock(:,14); | ||
| + | %cdom=datablock(:,15); | ||
| + | cdom(1:length(scan)) = NaN; | ||
| + | batt=datablock(:,15); | ||
| + | xmiss=datablock(:,16); | ||
| + | </ul> | ||
| + | |||
| + | ADCP | ||
| + | <ul> | ||
| + | Pitch = AnP100thDeg *.01; | ||
| + | Roll = AnR100thDeg *.01; | ||
| + | East_u = SerEmmpersec * 0.1; % convert mm per sec to cm per sec | ||
| + | North_v = SerNmmpersec * 0.1; | ||
| + | Vert_w = SerVmmpersec * 0.1; | ||
| + | VelError = SerErmmpersec * 0.1; | ||
| + | Mag = SerMagmmpersec * 0.1; | ||
| + | DIR = SerDir10thDeg * 0.1; | ||
| + | </ul> | ||
| + | </pre> | ||
| + | |||
| + | Update: I've started working on matching them up with the CSDMS variables via a [https://docs.google.com/spreadsheets/d/1IUTSWAHs2Rr5Fuuo0POPF1dQcB_Uhty4p1ZFURMpVE8/edit?usp=sharing Google spreadsheet]. It turns out that I don't know what specifically some of my variables are (conductivity for example: electrical or thermal?). I also don't see anything in there about light attenuation (PAR, turbidity). There's chlorophyll, but apparently only as measured via diatoms and not all phytoplankton. Dissolved oxygen seems to be missing, as are nutrients in general (nitrogen, phosphates) as is anything involving particulates (colored dissolved organic matter, gelbstoff, total suspended solids, etc). I might be looking in the wrong part of the list. Then there seems to be both a sea_water_flow__speed and a sea_water__flow_speed, and I'm not sure what the difference is. | ||
| + | |||
| + | In summary: it sounds like a simple task, but actually involves looking a lot of things up in detail, and can potentially be time-consuming. | ||
| + | |||
| + | Whatever the final released version of the CSDMS dictionary is, it needs to provide links to what everything means on each item in the list. | ||
| + | |||
<!-- Add any wiki Text above this Line --> | <!-- Add any wiki Text above this Line --> | ||
<!-- Do NOT Edit below this Line --> | <!-- Do NOT Edit below this Line --> | ||
{{#set: | {{#set: | ||
Expertise=Open_science| | Expertise=Open_science| | ||
| + | Expertise=Geosciences| | ||
Owner=Mimi_Tzeng| | Owner=Mimi_Tzeng| | ||
| − | Progress= | + | Progress=60| |
StartDate=2015-04-18| | StartDate=2015-04-18| | ||
TargetDate=2015-05-01| | TargetDate=2015-05-01| | ||
Type=Low}} | Type=Low}} | ||
Latest revision as of 21:16, 1 July 2015
Details on how to do this task: Document domain characteristics
As I understand this task, we are to take all of the variables used in the project and find the corresponding variable names from the CSDMS list. So to start, here are lists of all of my variables. I'm just going to directly copy-paste from my scripts (MOORprocess_all.m and MoorADCP.m) for starters. I imagine the publication-ready version of this will be in three columns: the "common" name of the variable as oceanographers would understand it, the name of the variable in my code, and the name of the variable in the CSDMS.
YSI
<ul>
ctddepth{3} = YSI(:,6);
ctdsal{3} = YSI(:,7);
ctdtemp{3} = YSI(:,8);
ctdpress{3} = YSI(:,9);
%ctdpress{3}(1:length(ctdtimestamp{3})) = NaN;
ctdcond{3} = YSI(:,10);
ctdspcond{3} = YSI(:,11);
ctdoxy{3} = YSI(:,13);
ctdoxysat{3} = YSI(:,14);
%ctdchla{3} = YSI(:,?);
%ctdturb{3} = YSI(:,15);
ctdturb{3}(1:length(ctdtimestamp{3})) = NaN; % a kludge for nonexistent variables in an existing package
ctdtds{3} = YSI(:,15);
</ul>
CTDs
<ul>
ctdtemp{r} = CTD(:,1);
ctdcond{r} = CTD(:,2);
ctdpress{r} = CTD(:,3);
ctdsal{r} = CTD(:,4);
ctdsound{r} = CTD(:,5);
ctdjday = CTD(:,6); %coming in, jday is Jan 1 = Day 1
ctddens{r} = CTD(:,8);
ctddepth{r} = CTD(:,9);
ctdspcond{r} = CTD(:,10);
</ul>
Thermistors
<ul>
tempT{r} = dataT(:,1);
pressT = dataT(:,2);
depthT = cnv(:,2);
</ul>
CTD cast
<ul>
depth=datablock(:,3);
sal=datablock(:,4);
temp=datablock(:,5);
dens=datablock(:,6);
press=datablock(:,7);
cond=datablock(:,8);
spcond=datablock(:,9);
oxy=datablock(:,10);
oxysat=datablock(:,11);
ph=datablock(:,12);
chla=datablock(:,13);
par=datablock(:,14);
%cdom=datablock(:,15);
cdom(1:length(scan)) = NaN;
batt=datablock(:,15);
xmiss=datablock(:,16);
</ul>
ADCP
<ul>
Pitch = AnP100thDeg *.01;
Roll = AnR100thDeg *.01;
East_u = SerEmmpersec * 0.1; % convert mm per sec to cm per sec
North_v = SerNmmpersec * 0.1;
Vert_w = SerVmmpersec * 0.1;
VelError = SerErmmpersec * 0.1;
Mag = SerMagmmpersec * 0.1;
DIR = SerDir10thDeg * 0.1;
</ul>
Update: I've started working on matching them up with the CSDMS variables via a Google spreadsheet. It turns out that I don't know what specifically some of my variables are (conductivity for example: electrical or thermal?). I also don't see anything in there about light attenuation (PAR, turbidity). There's chlorophyll, but apparently only as measured via diatoms and not all phytoplankton. Dissolved oxygen seems to be missing, as are nutrients in general (nitrogen, phosphates) as is anything involving particulates (colored dissolved organic matter, gelbstoff, total suspended solids, etc). I might be looking in the wrong part of the list. Then there seems to be both a sea_water_flow__speed and a sea_water__flow_speed, and I'm not sure what the difference is.
In summary: it sounds like a simple task, but actually involves looking a lot of things up in detail, and can potentially be time-consuming.
Whatever the final released version of the CSDMS dictionary is, it needs to provide links to what everything means on each item in the list.
