tgarciabotero/fluegg

A three-dimensional Lagrangian model capable of evaluating the influence of flow velocity, shear dispersion and turbulent diffusion on the transport and dispersal patterns of Asian carp eggs is presented. The model’s variables include not only biological behavior (growth rate, density changes) but also the physical characteristics of the flow field, such as mean velocities and eddy diffusivities.

Fluvial Egg Drift Simulator (FluEgg)

A three-dimensional Lagrangian model capable of evaluating the influence of flow velocity, shear dispersion and turbulent diffusion on the transport and dispersal patterns of Asian carp eggs is presented. The models variables include not only biological behavior (growth rate, density changes) but also the physical characteristics of the flow field, such as mean velocities and eddy diffusivities.

Code Structure

The Graphical User Inter Interface (GUI) code for the FluEgg is FluEgg.m and FluEgg.fig. The Main function of FluEgg is called FluEgggui, this function uses the Jump function, in this function particles move (jump) every time step following the random walk and random displacement approach.

Motivation

The transport of Asian carp eggs and fish in the early stages of development is very important on their life history and recruitment success. A better understanding of the transport and dispersal patterns of Asian carp at early life stages might give insight into the development and implementation of control strategies for Asian carp.

The FluEgg model was developed to evaluate the influence of flow velocity, shear dispersion and turbulent diffusion on the transport and dispersal patterns of Asian carp eggs. FluEgg output includes the three-dimensional location of the eggs at each time step together with its growth stage. The output results can be used to estimate lateral, longitudinal or vertical egg distribution. In addition, it can be used to generate an egg breakthrough curve (egg concentration as a function of time) at a certain downstream location from the virtual spawning location. Egg breakthrough curves are important for understanding egg dispersion and travel times. Egg vertical concentration distribution might give insights into egg suspension and settlement. Egg longitudinal concentration distributions can be used to estimate the streamwise and shear velocity, and minimum river length required for successful egg development.

Egg lateral distributions give information about dead zones, provided the input hydraulic data for the model is sufficiently well described. The location of suitable spawning grounds can be predicted based on the egg growth stage and on the vertical, lateral or longitudinal egg concentration distributions. The FluEgg model has the capability to predict the drifting behavior of eggs based on the physical properties of the eggs and the environmental and hydrodynamic characteristics of the stream where the eggs are drifting. A complete description of the FluEgg model was presented by Garcia et al. (2013); users can refer to this paper for detailed information on both the mathematical model and the performance of the model.

#References Garcia, T., Jackson, P.R.,Murphy, E.A., Valocchi, A.J., Garcia, M.H., 2013. Development of a Fluvial Egg Drift Simulator to evaluate the transport and dispersion of Asian carp eggs in rivers. Ecol. Model. 263, 211–222

Installation

The FluEgg model iswritten in the MATLAB® programming language (Mathworks, Natick, MA,USA). It requires the statistics and image processing toolboxes.

============================================================================== FluEgg Release License

%============================================================================== % FluEgg -Fluvial Egg Drift Simulator %============================================================================== % Copyright (c) 2013 Tatiana Garcia

% This program is free software: you can redistribute it and/or modify % it under the terms of the GNU General Public License version 3 as published by % the Free Software Foundation (currently at http://www.gnu.org/licenses/agpl.html) % with a permitted obligation to maintain Appropriate Legal Notices.

% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
% GNU General Public License for more details.

% You should have received a copy of the GNU General Public License
% along with this program.  If not, see <http://www.gnu.org/licenses/>.

============================================================================== DISCLAIMER

Unless otherwise noted below, this software is in the public domain because it contains materials that originally came from the United States Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at:

http://www.usgs.gov/visual-id/credit_usgs.html#copyright

Although this software program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.

This software is provided "AS IS."

Attributions and Licences: References to or use of non-U.S. Department of the Interior (DOI) products does not constitute an endorsement by the DOI.

This information is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The information has not received final approval by the USGS and is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the information.

============================================================================== Copyrights and Licenses for Third Party Software Distributed with FluEgg:

The FluEgg program contains code written by third parties. Such software will have its own individual LICENSE.TXT file in the directory in which it appears. This file will describe the copyrights, license, and restrictions which apply to that code.

The disclaimer of warranty in thid Open Source License applies to all code in the FluEgg Distribution, and nothing in any of the other licenses gives permission to use the names of Tatiana Garcia, U.S Geological Survey to endorse or promote products derived from this Software.

The following pieces of software have additional or alternate copyrights, licenses, and/or restrictions:

Program/Function Developer Directory Notes

---

FluEgg 1.3 Tatiana Garcia, University of Illinois FluEgg_Git_Repo\license_FluEgg_1.3.txt voxel.m Suresh Joel FluEgg_Git_Repo\voxel.m
cells.m Suresh Joel FluEgg_Git_Repo\voxel.m
dlmcell Roland Pfister FluEgg_Git_Repo\dlmcell.m Used in FluEgggui.m parseArgs.m Aslak Grinsted FluEgg_Git_Repo\parseArgs.m Used in Subaxis.m subaxis.m Aslak Grinsted FluEgg_Git_Repo\subaxis.m This function is used to reduce spacing between figure border and figure axis savefast.m Timothy E. Holy FluEgg_Git_Repo\savefast.m Used in FluEgggui.m pcscurvature.m Inci-Burak Güneralp,Prolific Oven,Palo Alto,CA FluEgg_Git_Repo\pcscurvature.m Used in google_earth.m-->Parametric cubic spline interpolation of digitized data points of meandering rivers reorient.m Inci-Burak Güneralp,Prolific Oven,Palo Alto,CA FluEgg_Git_Repo\reorient.m Used in pcscurvature.m savitzkyGolayFilt.m R. Losada FluEgg_Git_Repo\savitzkyGolayFilt.m Used in pcscurvature.m savitzkyGolay.m Jianwen Luo,Tsinghua University FluEgg_Git_Repo\savitzkyGolay.m Used in savitzkyGolayFilt.m deg2utm.m Rafael Palacios,Universidad Pontificia Comillas FluEgg_Git_Repo\deg2utm.m Used in google_earth.m-->Function to convert lat/lon vectors into UTM coordinates GEplot_3D.m Modif by P.R. Jackson and Tatiana Garcia FluEgg_Git_Repo\GEplot_3D.m Used in google_earth.m. Initial version (GEplot) developed by Rafael Palacios, Universidad Pontificia Comillas. kml2struct.m James Slegers Used in google_earth.m sn2xy.m FluEgg_Git_Repo\sn2xy_License.txt Used in google_earth.m-->Transform curvilinear orthogonal to cartesian coordinates utm2deg.m Rafael Palacios,Universidad Pontificia Comillas FluEgg_Git_Repo\deg2utm.m Used in google_earth.m and GEplot_3D-->Function to convert vectors of UTM coordinates into Lat/Lon vectors (WGS84).

fluegg's Issues

Select plan in Import Ras data

User should be able to pick Plan from drop list menu. As today, FluEgg imports the current plan in HECRAS project, not the one chosen from the menu.

Simulation time boxes not working

Calendar button doesn't work and can't manually edit the Start /End Date

HEC-RAS profile: ALL PROFILES (stuck)

In Edit River Input File window, when shifting from Time Series to Import HEC-RAS the HEC-RAS profile pop-up list button stays on ALL PROFILES. Three issues here:

1. Time Series default HEC-RAS profile value should be empty until something is loaded.
2. Time Series HEC-RAS profile should stick to All profiles -unsteady flow
3. When back to Import HEC-RAS I should get empty if nothing is loaded or All profiles -unsteady flow by default

Hydrograph Legends and Axis labels not showing

I've nor been able to display a Legend and axis label ('Time', 'Flow/water depth') in plot. Either the legend with line symbols.

This problem is for: plotProfiles(), plotTS, and plot_obs_data()

Egg vertical concentration distribution

When user wants to generate an egg vertical concentration distribution for a simulation using inverse model-->
We need to add a warning saying "This tool is not available for the inverse model"
--> or modify the code to account for eggs going in the opposite direction

Ending time of unsteady flow modeling in main FluEgg GUI need to be updated when simulation time changes

Instructions to compile FluEgg needed

Need to create a .PRJ file with specifications to compile a new standalone executable of FluEgg

plot hydrographs: Axis not properly scaled when zoomed in

X-Axis (dates) are not scaled properly when zooming in the hydrographs plot. It seems to me that the start and end dates are preserved even when zoomed into a shorter period.
Needs to update start and end dates according to scale

Bad time Axis in Import HEC-RAS

Check x-axis in Plot

Matlab Crashes when loading some .prj

For some .prj files, FLUEGG crashes without a warning nor error message after click on Load HEC-RAS Project button.
Need to isolate problematic line (for instance with a try-catch) and avoid execution if there is an Error.
Possible cause is a corrupted HECRAS project.

Load River Input Data initialization

Immediately after clicking "Load River Input Data file", I get the error message in Matlab:

Struct contents reference from a non-struct array object.

Error in FluEgg>Load_River_Input_Callback (line 89)
set(handles.Summary_panel,'Visible','on');
...

Model Evaluation: Loading HECRAS Data w.o. Observed data

Load River Input File > Model Evaluation
No Observed data specified.
Click at Import Data buttonm returns the error message:

Reference to non-existent field 'strObsDataFile'.

Error in Edit_River_Input_File>Import_data_button_Callback/import_OBS (line 929)
fileName = handles.strObsDataFile;

Checkbox Flow activated when it shouldn't

popup_HECRAS_profile_Callback() activates the checkbox_flow button when first in list of profiles (all profiles-unsteady flows) is selected. Even if Depth checkbox is already selected. That, shouldn't happen.

Make sure setting up spawning time and delete spawning time are inactivated in evaluation of HEC-RAS

results folder and log.txt file

This folder is not tracked in GIT. Add a line of code to create a results folder in the local FluEgg_USGS folder if it doesn't already exist. Otherwise do nothing. The log.txt file is created automatically by FluEgg as long as the folder \results exists.

Wiki updates

Wikipage:

FluEgg > Load river input File > Model Evaluation

becomes

FluEgg > Load river input File > HEC-RAS Evaluation

Select Plan in HEC-RAS Evaluation

Program only import data current Plan in HEC-RAS project, not the one selected from popup menu in FluEgg.
User should be able to select Plan to Import from FluEgg

Delete spawning time button not working in River Input file

Active (blue) Tabs simultaneously

When the Edit River Input File window is called, the Import HEC-RAS and Time Series Analysis tabs are blue (active)
The only active tab by default should be Import HEC-RAS tab

FluEgg.git folder in github

@tgarcia-usgs please remove this useless folder.
When the repo is cloned this folder is copied to the new repo.
Cheers!