Checking for non-preferred file/folder path names (may take a long time depending on the number of files/folders) ...

Agua Salud Discharge Data

Owners: This resource does not have an owner who is an active HydroShare user. Contact CUAHSI ( for information on this resource.
Type: Resource
Storage: The size of this resource is 163.8 MB
Created: Sep 22, 2020 at 3:47 p.m.
Last updated: Oct 14, 2020 at 7:46 p.m.
DOI: 10.4211/hs.282177bd87e7426e92899058f075359a
Citation: See how to cite this resource
Sharing Status: Published
Views: 1356
Downloads: 174
+1 Votes: 1 other +1 this
Comments: No comments (yet)


This resource contains 5-minute discharge data from 13 experimental catchments in Central Panama. The Agua Salud Project is managed by the Smithsonian Tropical Research Institute to facilitate research into the ecosystem benefits of various land covers in the humid tropics. The attached includes a more thorough description of this dataset and site specific details. A user can export these data from the HDF archive using the included Python script or access the data directly using a variety of HDF libraries in other languages.

Subject Keywords



Coordinate System/Geographic Projection:
WGS 84 EPSG:4326
Coordinate Units:
Decimal degrees
Place/Area Name:
Agua Salud, Panama
North Latitude
East Longitude
South Latitude
West Longitude


Start Date:
End Date:


Export Agua Salud Discharge Data

Use to extract discharge data with metadata from the Agua Salud Discharge HDF5 data archive.

Data Description

The AguaSaludDischarge.h5 file contains volumetric discharge data collected as part of the Panama Canal Watershed Experiment: Agua Salud Project. The file contains accumulated 5-minute instantaneous discharge measurements for each experimental watershed.


We used two-stage V-notch weirs equipped with pressure transducers to collect 5-minute discharge measurements. Each two-stage weir consisted of a concrete short-crested high-flow weir and a metal sharp-crested low-weir. We used non-vented In-Situ LevelTROLL pressure transducers with integrated data loggers to record instantaneous pressure measurements every 5 minutes. A field technician retrieved pressure measurements monthly and measured depth behind each weir using a staff gage. We collected barometric pressure data using an In-Situ BaroTROLL and removed daily barometric pressure fluctuations from the water pressure records. We used a Time Series Data Editor developed by AquaVeo as part of the Watershed Modeling System to convert pressure measurements to stage using field observed staff gage measurements. We used time series decomposition to remove systematic errors due to ephemeral woody debris clogging the weirs and sensor drift. We used discharge coefficients from Ogden et al., 2017 to convert stage measurements to discharge accounting for sedimentation.

Site Description

Elevation Map Landcover Map


python 3.6+



In a python3 enivronment:

python3 -m pip install h5py
python3 [options]


Download and install Anaconda3. Open the script in Spyder. Select Run > Configuration per file... Select the checkmark next to Command line options: and enter command line arguments in the text field. Select Run.

CUAHSI JupyterHub

These data are available for download from HydroShare with a HydroShare account. To export these data from a web browser using CUAHSI JupyterHub go to the resource landing page located here after signing into your Hydroshare account. Select Open with... on the right side of the landing page. Select CUAHSI JupyterHub. Read and accept the terms of use to sign-in with your Hydroshare account. Authorize read and write permissions. Select the Python 3.7 - Scientific server and Start. Find the drop down on the right labeled New and select Terminal. Navigate to ~/downloads/282177bd87e7426e92899058f075359a/282177bd87e7426e92899058f075359a/data/contents. From here you can export data using python3 [options].


usage: [-h] [-s S] [-d D] [-f [F]] [-ls] [-ld] [-ht]
                        [-o O] [-nd ND] [--first FIRST] [--last LAST]

Export binary Agua Salud data to CSV

optional arguments:
-h, --help     show this help message and exit
-s S           site
-d D           dataset
-f [F]         HDF5 input file [default: AguaSaludDischarge.h5]
-ls            list available sites with engineering code and exit
-ld            list datasets for a given site and exit
-ht            print input file hierarchy in tree format and exit
-o O           optional output filename
-nd ND         no data value [default: -9999.9]
--first FIRST  [YYYY-MM-DDThh:mmZ] datetime of first measurement to export
--last LAST    [YYYY-MM-DDThh:mmZ] datetime of last measurement export


$ python3 -s FOR -d discharge_sharp --first 2010-01-01T01:00Z --last 2010-01-02T01:00Z
Site: FOR
Dataset: discharge_sharp
Start export: 2010-01-01 01:00:00
End export: 2010-01-02 01:00:00
Exporting 289 measurements...
Wrote output data to FOR_discharge_sharp.csv

Sample output

# site: FOR
# dataset: discharge_sharp
# drainage_area: 144.87 hectares [ha]
# weir_latitude: 9.20893° [wgs84]
# weir_longitude: -79.7795° [wgs84]
# no_data_value: -9999.9
# engr_code: V02ASL
# description: Stream discharge over sharp-crested weir
# datetime: Instantaneous measurement time - ISO 8601 Standard date-time string YYYY-MM-DD hh:mmZ
# discharge: Stream discharge over weir in cubic meters per second [m^3 s^-1]
# quality: Numerical flag indicating sharp-crested weir measurement quality
# -1: No data
# 0 : Depth is within limits of weir box
# 2 : Flow deviation greater than 1 liter per second from short-crested weir
# 3 : Flow depth exceeded weir maximum depth of V-notch
2010-01-01 01:00Z,-9999.9,2

Data hierarchy and available date ranges



The hierarchical data structure is grouped by site. The top-level site below root is /site_data/. Below /site_data/ are 13 groups corresponding to each experimental watershed.


Each of the site-corresponding groups contains 3 or 6 datasets. depth_short is a 1-dimensional array containing depth measurements above the invert of a high-flow short-crested weir. depth_sharp is a 1-dimensional array of depth measurments above the invert of a low-flow sharp-crested weir. discharge_short is a 1-dimensional array of discharge measurements derived using a weir rating curve and depth_short measurements. discharge_sharp is a 1-dimensional array of discharge measurements derived from depth_sharp. field_discharge_short and field_discharge_sharp contain field observed measurements of depth with correspondingly derived discharge for both short and sharp-crested weirs.

$ python3 -ht
├── ARN/
│   ├── depth_short (2016-04-22T17:30Z to 2018-01-29T15:20Z)
│   ├── depth_sharp (2016-04-22T17:30Z to 2018-01-29T15:20Z)
│   ├── discharge_short (2016-04-22T17:30Z to 2018-01-29T15:20Z)
│   ├── discharge_sharp (2016-04-22T17:30Z to 2018-01-29T15:20Z)
│   ├── field_discharge_short (2016-04-22T17:00Z to 2018-01-29T15:00Z)
│   └── field_discharge_sharp (2016-05-12T17:00Z to 2017-08-08T15:00Z)
├── COF/
│   ├── depth_short (2014-12-10T18:15Z to 2018-02-19T17:35Z)
│   ├── discharge_short (2014-12-10T18:15Z to 2018-02-19T17:35Z)
│   └── field_discharge_short (2014-12-10T18:00Z to 2018-02-19T17:00Z)
├── CTD/
│   ├── depth_short (2015-05-29T15:30Z to 2018-04-09T15:10Z)
│   ├── discharge_short (2015-05-29T15:30Z to 2018-04-09T15:10Z)
│   └── field_discharge_short (2015-05-29T15:00Z to 2018-04-09T15:00Z)
├── CUT/
│   ├── depth_short (2016-04-22T16:00Z to 2018-04-09T15:25Z)
│   ├── depth_sharp (2016-04-22T16:00Z to 2018-04-09T15:25Z)
│   ├── discharge_short (2016-04-22T16:00Z to 2018-04-09T15:25Z)
│   ├── discharge_sharp (2016-04-22T16:00Z to 2018-04-09T15:25Z)
│   ├── field_discharge_short (2016-04-22T16:00Z to 2018-04-09T15:00Z)
│   └── field_discharge_sharp (2016-05-24T17:00Z to 2018-04-09T15:00Z)
├── FOR/
│   ├── depth_short (2009-03-20T14:45Z to 2018-03-22T16:25Z)
│   ├── depth_sharp (2009-03-20T14:45Z to 2018-03-22T16:25Z)
│   ├── discharge_short (2009-03-20T14:45Z to 2018-03-22T16:25Z)
│   ├── discharge_sharp (2009-03-20T14:45Z to 2018-03-22T16:25Z)
│   ├── field_discharge_short (2009-03-20T15:00Z to 2018-03-22T16:00Z)
│   └── field_discharge_sharp (2009-03-20T14:00Z to 2017-03-08T15:00Z)
├── MOS/
│   ├── depth_short (2009-03-27T17:55Z to 2018-03-16T15:50Z)
│   ├── depth_sharp (2009-03-27T17:55Z to 2018-03-16T15:50Z)
│   ├── discharge_short (2009-03-27T17:55Z to 2018-03-16T15:50Z)
│   ├── discharge_sharp (2009-03-27T17:55Z to 2018-03-16T15:50Z)
│   ├── field_discharge_short (2009-03-27T17:00Z to 2018-03-16T15:00Z)
│   └── field_discharge_sharp (2009-04-02T15:00Z to 2017-06-07T16:00Z)
├── NAT/
│   ├── depth_short (2009-03-07T21:30Z to 2018-02-05T17:05Z)
│   ├── depth_sharp (2009-03-07T21:30Z to 2018-02-05T17:05Z)
│   ├── discharge_short (2009-03-07T21:30Z to 2018-02-05T17:05Z)
│   ├── discharge_sharp (2009-03-07T21:30Z to 2018-02-05T17:05Z)
│   ├── field_discharge_short (2009-03-07T21:00Z to 2018-02-05T17:00Z)
│   └── field_discharge_sharp (2009-04-21T15:00Z to 2018-02-05T17:00Z)
├── PAS/
│   ├── depth_short (2009-03-07T19:00Z to 2018-02-07T15:05Z)
│   ├── depth_sharp (2009-03-07T19:00Z to 2018-02-07T15:05Z)
│   ├── discharge_short (2009-03-07T19:00Z to 2018-02-07T15:05Z)
│   ├── discharge_sharp (2009-03-07T19:00Z to 2018-02-07T15:05Z)
│   ├── field_discharge_short (2009-03-07T19:00Z to 2018-02-07T15:00Z)
│   └── field_discharge_sharp (2009-03-07T20:00Z to 2018-02-07T14:00Z)
├── RAS/
│   ├── depth_short (2009-03-20T16:50Z to 2018-01-24T17:45Z)
│   ├── depth_sharp (2009-03-20T16:50Z to 2018-01-24T17:45Z)
│   ├── discharge_short (2009-03-20T16:50Z to 2018-01-24T17:45Z)
│   ├── discharge_sharp (2009-03-20T16:50Z to 2018-01-24T17:45Z)
│   ├── field_discharge_short (2009-03-27T14:00Z to 2018-01-24T17:00Z)
│   └── field_discharge_sharp (2009-03-20T16:00Z to 2009-03-20T16:00Z)
├── SAC/
│   ├── depth_short (2009-06-17T16:55Z to 2018-03-23T16:45Z)
│   ├── depth_sharp (2009-06-17T16:55Z to 2018-03-23T16:45Z)
│   ├── discharge_short (2009-06-17T16:55Z to 2018-03-23T16:45Z)
│   ├── discharge_sharp (2009-06-17T16:55Z to 2018-03-23T16:45Z)
│   ├── field_discharge_short (2009-06-17T16:00Z to 2018-03-23T16:00Z)
│   └── field_discharge_sharp (2009-07-28T21:00Z to 2017-07-28T15:00Z)
├── SEC/
│   ├── depth_sharp (2009-04-23T18:00Z to 2018-02-05T16:55Z)
│   ├── discharge_sharp (2009-04-23T18:00Z to 2018-02-05T16:55Z)
│   └── field_discharge_sharp (2009-04-23T18:00Z to 2018-02-05T16:00Z)
├── TEK/
│   ├── depth_short (2009-01-17T21:20Z to 2018-02-08T16:15Z)
│   ├── depth_sharp (2009-01-17T21:20Z to 2018-02-08T16:15Z)
│   ├── discharge_short (2009-01-17T21:20Z to 2018-02-08T16:15Z)
│   ├── discharge_sharp (2009-01-17T21:20Z to 2018-02-08T16:15Z)
│   ├── field_discharge_short (2009-01-17T21:00Z to 2018-02-08T16:00Z)
│   └── field_discharge_sharp (2009-04-22T15:00Z to 2017-08-28T17:00Z)
└── TKU/
    ├── depth_short (2009-04-07T16:15Z to 2018-02-08T15:05Z)
    ├── depth_sharp (2009-04-07T16:15Z to 2018-02-08T15:05Z)
    ├── discharge_short (2009-04-07T16:15Z to 2018-02-08T15:05Z)
    ├── discharge_sharp (2009-04-07T16:15Z to 2018-02-08T15:05Z)
    ├── field_discharge_short (2009-04-14T13:00Z to 2018-02-08T15:00Z)
    └── field_discharge_sharp (2009-04-07T16:00Z to 2017-08-28T18:00Z)

These datasets contain arrays of compound data types typically consisting of three components: a null-terminated ASCII character string containing an ISO 8601 formatted datetime, a 32-bit float containing a measurement value, and a 32-bit integer containing a quality code. Associated attributes are added to output CSV files as commented header lines by default when using


Each group and dataset has a number of metadata attributes with full descriptions. The data format, contents, and metadata can be explored using h5dump.

$ h5dump -A -d /site_data/ARN/discharge_sharp AguaSaludDischarge.h5
HDF5 "AguaSaludDischarge.h5" {
DATASET "/site_data/ARN/discharge_sharp" {
    H5T_STRING {
        STRSIZE 18;
        CTYPE H5T_C_S1;
    } "datetime";
    H5T_IEEE_F32LE "discharge";
    H5T_STD_I32LE "quality";
DATASPACE  SIMPLE { ( 186311 ) / ( 186311 ) }
ATTRIBUTE "datetime" {
        STRSIZE 86;
        CTYPE H5T_C_S1;
    DATA {
    (0): "Instantaneous measurement time - ISO 8601 Standard date-time string YYYY-MM-DD hh:mmZ\000"
ATTRIBUTE "description" {
        STRSIZE 41;
        CTYPE H5T_C_S1;
    DATA {
    (0): "Stream discharge over sharp-crested weir\000"
ATTRIBUTE "discharge" {
        STRSIZE 65;
        CTYPE H5T_C_S1;
    DATA {
    (0): "Stream discharge over weir in cubic meters per second [m^3 s^-1]\000"
ATTRIBUTE "engr_code" {
        STRSIZE 7;
        CTYPE H5T_C_S1;
    DATA {
    (0): "V13ASL\000"
ATTRIBUTE "no_data_value" {
    DATA {
    (0): -9999.9
ATTRIBUTE "quality" {
        STRSIZE 246;
        CTYPE H5T_C_S1;
    DATA {
    (0): "Numerical flag indicating sharp-crested weir measurement quality
        -1: No data
        0 : Depth is within limits of weir box
        2 : Flow deviation greater than 1 liter per second from short-crested weir
        3 : Flow depth exceeded weir maximum depth of V-notch

Related Resources

This resource belongs to the following collections:
Title Owners Sharing Status My Permission
Agua Salud Hydrometric Data Jason Regina · Fred Ogden  Published Open Access
Agua Salud Hydrometric Data Jason Regina  Published Open Access
Agua Salud Hydrometric Data Jason Regina  Published Open Access


Funding Agencies

This resource was created using funding from the following sources:
Agency Name Award Title Award Number
Stanley Motta
Hoch Trust
National Science Foundation Collaborative Research: Planning And Land Management in Tropical Ecosystem; Complexities of land-use and hydrology coupling in the Panama Canal Watershed 1360305, 1360369, 1360384, 1360391
Smithsonian Tropical Research Institute
HSBC Climate Partnership (2008-2012)
Levinson Family Foundation

How to Cite

Regina, J. A., F. L. Ogden, J. S. Hall, R. F. Stallard (2020). Agua Salud Discharge Data, HydroShare,

This resource is shared under the Creative Commons Attribution CC BY.


There are currently no comments

New Comment