mohid studio - user guide

ACTION MODULERS

MOHID Studio User Guide

User Guide for MOHID Studio Express and Professional Edition

Frank Braunschweig Luis Fernandes Filipe Lourenço

September 2010

(Revision December 2010)

This document is the MOHID Studio User Guide. It contains explanation of all

features and tools of MOHID Studio.

This document makes part of the MOHID Studio Documentation.

M O H I D S t u d i o – U s e r G u i d e

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Index

1 PREFACE 1

1.1 Copyright 1

1.2 Warranty 1

1.3 Further Information 1

2 INTRODUCTION 2

2.1 Features 2

2.2 Backward compatibility 2

2.3 MOHID in Action 2

2.4 MOHID Studio Editions 3

2.5 Concepts behind MOHID Studio 4

2.6 Starting MOHID Studio 5

2.7 Main Window 5

2.7.1 Dockable Windows 6

2.7.2 Main Menu 7

2.8 Home menu 7

2.9 Getting Started with MOHID Studio 8

2.10 Workspaces 9

2.10.1 Introduction to Workspaces 9

2.10.2 Working with Workspaces 9

2.10.3 Managing Workspaces 11

3 PROJECT MANAGEMENT 12

3.1 Solution 14

3.1.1 Creating or opening solutions 14

3.1.2 Closing solutions 15


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3.1.3 Managing solutions 15

3.1.4 Exporting solutions 15

3.1.5 Importing solution 16

3.2 Domains 17

3.2.1 Creating domains 17

3.2.2 Domain properties 19

3.2.3 Removing domains 19

3.2.4 Managing domains 19

3.2.5 Nested domains 20

3.3 Simulations 21

3.3.1 Creating simulations 21

3.3.2 Simulation properties 22

3.3.3 Root and sequential simulation 22

3.3.4 Removing simulations 24

3.3.5 Files associated to simulation 24

3.3.6 Copying simulation data files 25

3.3.7 Cleaning simulation result files 25

3.4 Organizing data files 25

3.4.1 Data files associated to simulations 25

3.4.2 Data files associated to domains 26

3.5 Editing data files 27

3.6 Executing Models 28

3.6.1 Executing a single simulation 28

3.6.2 Executing a set of simulations 28

3.6.3 Simulation progress 30

3.7 Visualizing results 31

3.7.1 Visualizing HDF results 32

3.7.2 Visualizing Time Series results 32

4 MAP VISUALIZATION (GIS) 33

4.1 Introduction 33

4.2 Date & Time 35


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4.3 Layers General Properties 36

4.4 Raster Layers 37

4.4.1 Raster Collections 37

4.4.2 WMS Layers 39

4.5 MOHID ASCII Layers 41

4.5.1 XYZ Points layer 42

4.5.2 Grid layer 43

4.5.3 Grid Data layer 44

4.5.4 Drainage Network layer 45

4.5.5 Polygons layer 46

4.6 HDF Files 47

4.6.1 Grid Map 47

4.6.2 Vector (Arrow) Map 48

4.6.3 Drainage Network Map 49

4.6.4 Lagrangian Particle Map 49

4.7 Other Vector Layers 49

4.7.1 ESRI Shapefiles Layers 50

4.7.2 XML Geometry Layers 50

4.7.3 HGT Layers 50

4.8 Monitoring Station Layers 51

4.9 Label Layers 51

4.10 Moving Layers 52

4.11 Layer Styles 52

4.11.1 Simple Vector Style 53

4.11.2 Gradient Layer Style 56

4.11.3 Transparency Layer Style 58

4.11.4 Classified Layer Style 59

4.11.5 Arrow Layer Style 61

4.11.6 Style Templates 63

4.12 Querying Data 63

4.13 Images 64


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5 GRAPH VISUALIZATION 65

5.1 Introduction 65

5.2 Graph Windows 66

5.2.1 Introduction 66

5.2.2 Create from MOHID ASCII Time Series File 67

5.2.3 Create from MOHID Studio’s database 67

5.2.4 Closing a Graph Window 67

5.2.5 Saving a graph window 67

5.2.6 Open a saved graph 67

5.2.7 Create from Explorer 68

5.3 Series 68

5.3.1 Adding Series 68

5.3.2 Removing Series 69

5.4 Graph Layout 69

5.4.1 Series layout 69

6 TIME SERIES MANAGER 70

6.1 Introduction 70

6.2 Environmental Monitoring menu 70

6.2.1 Parameters 70

6.2.2 Monitoring Station 72

6.2.3 Time Series 74

6.2.4 Importing and Exporting Time Series 76

6.2.5 Moving Time Series 78

6.2.6 Field Campaigns and Visited Points 79

6.2.7 Import from XLS Files 83

6.3 Reports 86

6.3.1 Report by Parameter 87

6.3.2 Report by Time Series 88

6.3.3 Report by Monitoring Station 89

6.3.4 Report by Min/Max Values 90

6.3.5 Report by Moving Time Series 91


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7 TOOLS 93

7.1 Introduction 93

7.2 Geometry Layer Tools 93


7.2.2 Named Points 94

7.2.3 Named Lines 94

7.2.4 Named Polygons 95

7.2.5 XYZ Points 96

7.3 Grid Tools 96


7.3.2 Constant Grid 97

7.3.3 Variable Spaced Grid 98

7.3.4 Refine Grid 98

7.4 Grid Data Tools 99


7.4.2 Creating Grid Data from Points 99

7.4.3 Creating Grid Data from Shapefiles 100

7.4.4 Modifying a Grid Data 101

7.5 Watershed Tools 102


7.5.2 Depression Removal 103

7.5.3 Watershed Delineation 104

7.5.4 Cross Section Definition 106

7.5.5 Soil Depth 107

7.6 Time Series Tools 108


7.6.2 Grid Time Series Location 108

7.6.3 Node Time Series Location 109

7.6.4 Time Series from Database 109

7.7 HDF File Tools 110


7.7.2 Create from Time Series 110

7.7.3 Interpolate HDF Files 110


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7.7.4 Vertical Cuts 111

7.8 Boxes 111


7.8.2 Create Boxes 112

8 FILE EXPORT / CONVERSIONS 113

8.1 Introduction 113

8.2 Export to KML 113

8.2.1 Export HDF Polygon to KML 113

8.2.2 Export Grid Data to KML 114

8.2.3 Export Drainage Network to KML 115

8.2.4 Export Named Geometry to KML 115

8.3 Export to ESRI Shapefile 116

8.3.1 Export HDF Polygon to Shapefile 116

8.3.2 Export Grid Data to Shapefile 116

8.3.3 Export Drainage Network to Shapefile 116

8.3.4 Export Named Geometry to Shapefile 116

8.4 Convert MOHID ASCII Geometries to XML Geometries 117

8.5 Convert XML Geometries to MOHID ASCII Geometries 117

9 ADMINISTRATION 119


9.2 License Management 119


9.2.2 License Manager 121

9.2.3 License Request 123

9.2.4 License Emission 124

9.2.5 License Validation 125

10 FILE FORMATS 126



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10.2 MOHID ASCII Files 127


10.2.2 XYZ Files 128

10.2.3 Line Files 129

10.2.4 Polygon Files 130

10.2.5 Grid Files 130

10.2.6 Grid Data Files 133

10.2.7 Drainage Network Files 134

10.2.8 Time Series Files 135

10.3 XML Files 137


10.3.2 XML Named Points Files 137

10.3.3 XML Named Lines Files 138

10.3.4 XML Named Polygon Files 139

10.4 Other Formats 139

10.4.1 HDF Files 139

10.4.2 ESRI Shapefiles 140


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Index of Tables

TABLE 1 : MOHID STUDIO LICENSE OVERVIEW 4

TABLE 2: EXAMPLES FOR ZOOM LEVELS (BLUE MARBLE IMAGE GALLERY) 38

TABLE 3: DISPLAY NUMERICAL FORMATS EXAMPLES 72

TABLE 4 : MOHID STUDIO LICENSE FEES (OCTOBER 2010) 121


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Index of Figures

FIGURE 2-1: EXECUTE MOHID STUDIO 5

FIGURE 2-2: MOHID STUDIO’S MAIN WINDOW 6

FIGURE 2-3: MOHID STUDIO’S MAIN WINDOW (SIDE BY SIDE DOCKING) 7

FIGURE 2-4: EXAMPLE OF A RIBBON MENU (MAP) 7

FIGURE 2-5: HOME MENU 8

FIGURE 2-6: CREATE A NEW WORKSPACE OR LOAD AN EXISTING ONE 10

FIGURE 2-7: SAVE WORKSPACE ON PROGRAM EXIT 10

FIGURE 2-8: MANAGING WORKSPACES 11

FIGURE 3-1: PROJECT MENU 12

FIGURE 3-2: EXPLORER WINDOW 13

FIGURE 3-3: ACCESSING PROJECT MANAGEMENT OPTIONS FROM THE CONTEXT MENU 14

FIGURE 3-4: CREATING A NEW SOLUTION 14

FIGURE 3-5: MANAGING SOLUTIONS 15

FIGURE 3-6: EXPORTING SOLUTIONS 16

FIGURE 3-7: IMPORTING SOLUTIONS 17

FIGURE 3-8: CREATING A NEW DOMAIN 18

FIGURE 3-9: DIRECTORY STRUCTURE FOR A DOMAIN 19

FIGURE 3-10: MANAGING DOMAIN 20

FIGURE 3-11: REMOVE DOMAIN 20

FIGURE 3-12: PROJECT TREE SHOWING A DOMAIN WITH A NESTED DOMAIN 21

FIGURE 3-13: CREATING A NEW SIMULATION 22

FIGURE 3-14: PROJECT TREE SHOWING ROOT AND SEQUENTIAL SIMULATION AND THE USAGE OF

BRANCHES 23

FIGURE 3-15: FILES ASSOCIATED TO SIMULATIONS 24

FIGURE 3-16: PROJECT TREE CONTEXT MENU TO PERFORM TASKS RELATED WITH THE GENERAL DATA

DIRECTORY 26

FIGURE 3-17: FILE EDITOR WITH TWO OPEN DATA FILES 27

FIGURE 3-18: SCHEDULING A SET OF SIMULATIONS 29

FIGURE 3-19: SCHEDULING NESTED DOMAINS 30

FIGURE 3-20: MODEL CONTROLLER WINDOW 30

FIGURE 3-21: MODEL SCREEN OUTPUT WINDOW 31

FIGURE 3-22: HDF LIST VIEW WITH COMMANDS 32

FIGURE 3-23: TIME SERIES LIST VIEW WITH COMMANDS 32

FIGURE 4-1: MAP MENU 33

FIGURE 4-2: MAP WINDOW 34

FIGURE 4-5: ACCESSING MAP OPTIONS FROM THE CONTEXT MENU 35


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FIGURE 4-3: DATE & TIME CONTROL 35

FIGURE 4-4: CURRENT TIME WINDOW 36

FIGURE 4-6: ADDING RASTER COLLECTIONS 37

FIGURE 4-7: DISPLAYING A RASTER LAYER IN MOHID STUDIO 39

FIGURE 4-8: ADDING WMS LAYER 40

FIGURE 4-9: DISPLAYING A WMS LAYER IN MOHID STUDIO 41

FIGURE 4-10: ADDING A XYZ POINT VECTOR LAYER 42

FIGURE 4-11: DISPLAYING A XYZ POINT LAYER 43

FIGURE 4-12: DISPLAYING A GRID LAYER 44

FIGURE 4-13: DISPLAYING A GRID DATA LAYER 45

FIGURE 4-14: DISPLAYING A DRAINAGE NETWORK LAYER 46

FIGURE 4-15: DISPLAYING A POLYGON LAYER 47

FIGURE 4-16: ADDING A GRID MAP VECTOR LAYER 47

FIGURE 4-17: DISPLAYING A VECTOR MAP 49

FIGURE 4-18: ADDING A HGT VECTOR LAYER 50

FIGURE 4-19: CREATING A LABEL LAYER 52

FIGURE 4-20: EDITING THE LAYER STYLE 53

FIGURE 4-21: CONFIGURING A SIMPLE VECTOR STYLE 55

FIGURE 4-22: SHOWING DIFFERENT SIMPLE VECTOR STYLES 56

FIGURE 4-23: CONFIGURING A GRADIENT LAYER STYLE 57

FIGURE 4-24: SHOWING A GRADIENT LAYER STYLE 58

FIGURE 4-25: CONFIGURING A TRANSPARENCY LAYER STYLE 58

FIGURE 4-26: SHOWING A TRANSPARENCY LAYER STYLE 59

FIGURE 4-27: CONFIGURING A CLASSIFIED LAYER STYLE 60

FIGURE 4-28: SHOWING A CLASSIFIED LAYER STYLE 61

FIGURE 4-29: CONFIGURING A ARROW LAYER STYLE 62

FIGURE 4-30: SHOWING AN ARROW LAYER STYLE 62

FIGURE 4-31: MANAGING STYLE TEMPLATES 63

FIGURE 4-32: QUERYING THE MAP 64

FIGURE 5-1: XY GRAPH MENU 65

FIGURE 5-2: XY GRAPH WINDOW 65

FIGURE 5-3: TIME SERIES SELECTION WINDOW 66

FIGURE 5-4: OPEN GRAPH WINDOWS FROM STUDIO EXPLORER 68

FIGURE 6-1: ENVIRONMENTAL MONITORING MENU 70

FIGURE 6-2: REPORTS MENU 70

FIGURE 6-3: PARAMETERS MANAGER 71

FIGURE 6-4: PARAMETERS PROPERTIES WINDOW 71

FIGURE 6-5: MONITORING STATION MANAGER 73


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FIGURE 6-6: MONITORING STATION PROPERTIES WINDOW 74

FIGURE 6-7: TIME SERIES MANAGER 75

FIGURE 6-8: TIME SERIES PROPERTIES WINDOW 76

FIGURE 6-9: IMPORT TIME SERIES WINDOW 77

FIGURE 6-10: EXPORT TIME SERIES WINDOW 78

FIGURE 6-11: MOVING TIME SERIES WINDOW 78

FIGURE 6-12: MOVING TIME SERIES PROPERTIES WINDOW 79

FIGURE 6-13: FIELD CAMPAIGN MANAGER WINDOW 80

FIGURE 6-14: FIELD CAMPAIGN PROPERTIES WINDOW 81

FIGURE 6-15: VISITED POINT PROPERTIES WINDOW 82

FIGURE 6-16: VISITED POINT MANAGER WINDOW 82

FIGURE 6-17: IMPORT TIME SERIES TEMPLATE 84

FIGURE 6-18: IMPORT TIME SERIES WINDOW 85

FIGURE 6-19: IMPORT BOAT CRUISE WINDOW 85

FIGURE 6-20: REPORT WINDOW – PARAMETER 86

FIGURE 6-21: REPORT WINDOW – SETTINGS 87

FIGURE 6-22: REPORT BY PARAMETER 88

FIGURE 6-23: REPORT WINDOW – TIME SERIES 89

FIGURE 6-24: REPORT WINDOW – MONITORING STATION 90

FIGURE 6-25: REPORT WINDOW – MIN/MAX VALUES 91

FIGURE 6-26: REPORT WINDOW – MOVING TIME SERIES 92

FIGURE 7-1: TOOL MENU 93

FIGURE 7-2: CREATING NAMED POINTS 94

FIGURE 7-3: CREATING NAMED LINES 95

FIGURE 7-4: CREATING NAMED POLYGONS 96

FIGURE 7-5: CREATING CONSTANT GRID 97

FIGURE 7-6: CREATING VARIABLE GRID 98

FIGURE 7-7: CREATING A GRID DATA FROM POINTS 100

FIGURE 7-8: CREATING A GRID DATA FROM SHAPEFILE (POLYGONS) 101

FIGURE 7-9: MODIFYING A GRID DATA 102

FIGURE 7-10: DEPRESSION REMOVAL TOOL 103

FIGURE 7-11: WATERSHED DELINEATION TOOL 105

FIGURE 7-12: CROSS SECTION DEFINITION TOOL 106

FIGURE 7-13: SOIL DEPTH TOOL 107

FIGURE 7-14: GRID TIME SERIES LOCATION TOOL 108

FIGURE 7-15: CREATING A TIME SERIES FROM THE DATABASE 109

FIGURE 7-16: INTERPOLATING A HDF FILE TO A NEW GRID 110

FIGURE 7-17: CREATING A VERTICAL CUT FROM 3D HDF FILE 111


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FIGURE 7-18: CREATING A BOXES FILE FROM A SET OF POLYGONS 112

FIGURE 8-1: EXPORT / CONVERSIONS MENU 113

FIGURE 8-2: EXPORT HDF TO KML 114

FIGURE 8-3: EXPORT GRID DATA TO KML 114

FIGURE 8-4: EXPORT DRAINAGE NETWORK TO KML 115

FIGURE 8-5: EXPORT NAMED GEOMETRY TO KML 115

FIGURE 8-6: CONVERT MOHID ASCII TO XML 117

FIGURE 8-7: CONVERT XML TO MOHID ASCII 118

FIGURE 9-1: ADMINISTRATION TAB – LICENSE MANAGER 122

FIGURE 9-2: ORB BUTTON – LICENSE MANAGER 122

FIGURE 9-3: LICENSE MANAGER – EVALUATION EDITION 123

FIGURE 9-4: LICENSE REQUEST FORM 124

FIGURE 9-5: LICENSE VALIDATION 125

FIGURE 9-6: LICENSE VALIDATION – VALIDATION KEY 126

FIGURE 10-1: EXAMPLE OF A MOHID ASCII FILE 128

FIGURE 10-2: EXAMPLE OF MOHID ASCII XYZ FILE 129

FIGURE 10-3: EXAMPLE OF A MOHID ASCII LINE FILE 129

FIGURE 10-4: EXAMPLE OF A MOHID ASCII POLYGON FILE 130

FIGURE 10-5: EXAMPLE GRIDS SUPPORTED BY MOHID 131

FIGURE 10-6: EXAMPLE OF A MOHID ASCII GRID FILE 133

FIGURE 10-7: EXAMPLE NODE DEFINITION 135

FIGURE 10-8: EXAMPLE REACH DEFINITION 135

FIGURE 10-9: EXAMPLE MOHID ASCII TIME SERIES FILE (SIMPLE) 136

FIGURE 10-10: EXAMPLE MOHID ASCII TIME SERIES FILE (ADVANCED) 137

FIGURE 10-11: A XML NAMED POINT FILE 138

FIGURE 10-12: A XML NAMED LINE FILE 138

FIGURE 10-13: A XML NAMED POLYGON FILE 139


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1 Preface

1.1 Copyright

This document refers to MOHID Studio, priority software protected by copyright. All

rights are reserved. Copying or other reproduction of this manual, or related documents,

is prohibited without prior written consent of Action Modulers, Consultores de

Segurança (Action Modulers).

MOHID Water Modelling System is priority software of the Technical University of

Lisbon.

1.2 Warranty

The warranty given by Action Modulers is limited as specified in your Software License

Agreement. Please note that numerical modeling software programs are very complex

system and may not be free of errors, so you are advised to validate your work. Action

Modulers shall not be responsible for any damage arising out of the use of this

document, MOHID Studio, MOHID Water Modelling System or any related program or

document.

1.3 Further Information

For further information about MOHID Studio please contact:

Action Modulers, Consultores de Segurança Lda.

Rua Cidade de Frehel, Bloco B, Nº 12 A

2640-469 Mafra, Portugal

Tel.: +351 261 813 660

Fax: +351 261 813 666

E-mail: [email protected]

Web: http://www.actionmodulers.com



2 Introduction

MOHID Studio is a graphical user interface for the MOHID Water Modelling System.

With MOHID Studio you can use MOHID Numerical Engines from inside a user

friendly environment, managing all tasks required in order to prepare, execute and

analyze results of numerical simulations done by MOHID Numerical Engines.

2.1 Features

MOHID Studio is an integrated system which permits to manage and edit data files,

create and launch simulations and analyze model results. Map data can be displayed

through an integrated GIS system and time series data can be displayed an integrated

graph visualization engine. A set of tools allows the user to create and preprocess

MOHID data files. A special module allows managing data from field campaigns and/or

automatic stations. MOHID Studio features also offer the possibility to convert data

among a set of common formats and MOHID internal formats. All features of MOHID

Studio are described along this user guide.

2.2 Backward compatibility

With all this features above mentioned MOHID Studio replaces the existing MOHID

graphical user interfaces, namely MOHID GUI, MOHID GIS, MOHID Time Series

Editor and MOHID Post Processor.

Backward compatibility allows importing projects created with MOHID GUI. Some

formats of MOHID ASCII files (points, lines and polygons) has been replaced by a new,

XML based, generic geometry format. Tools to convert from one format to another are

available.

2.3 MOHID in Action

MOHID Studio makes part of the MohidInAction toolkit. MohidInAction, developed and

maintained by Action Modulers, is a set of graphical user interface targeting the

MOHID Water Modelling System, including:

MOHID Studio – Graphical User Interface for MOHID Numerical Engines



Action Flood – Operational Flood Warning System based on MOHID Land

Action Beach – Operational Bathing Water Forecast System based on MOHID

Water

2.4 MOHID Studio Editions

After installing MOHID Studio it will work for 30 days for an evaluation period.

Evaluation versions have restricted usage. In order to work with a licensed version of

MOHID Studio, the user needs to register and request a license (for more information

read MOHID Studio – Installation Guide).

There are two types of licensed MOHID Studio versions: MOHID Studio Express and

MOHID Studio Professional. Licenses are distributed on a single machine basis. Action

Modulers may provide other types of licenses upon request.

MOHID Studio Express license is free of charge and it is valid for six month period.

After this period you need buy a MOHID Studio Professional license or renew your

MOHID Studio Express license, if you want to keep using MOHID Studio Express.

MOHID Studio Express works with all features enabled, but with some restriction

(check restrictions on Table 1).

MOHID Professional Edition works without any restriction. License fees vary in

function of the requested license.

Table 1 shows an overview of all MOHID Studio licenses.

On subsection 9.2.2 is explained how to get your license and how to validate it.



Feature MOHID Studio

Express

MOHID Studio

Professional

MOHID Studio

Professional Unlimited

MOHID Studio

Professional Enterprise

Number of single machines where license can be installed

1 1 1 5

Maximum number of layers which can be displayed in the GIS engine

3 unlimited unlimited unlimited

Maximum number of domains which can be created within a single workspace


Maximum number of scenarios which can be configured within a single workspace


Maximum number of nested domains which can be created


Maximum number of simultaneously opened XY Graph windows


Watermarks free images No Yes Yes Yes

License Period (month) 6 12 unlimited unlimited

Price (Euros) Free See note1

Table 1 : MOHID Studio License Overview

2.5 Concepts behind MOHID Studio

MOHID Studio uses a database to store all information about projects and data from

field campaigns and/or automatic stations. Data and result files from numerical models

are stores in a well defined directory structure.

1 During Beta Test license are distributed free of charge. Visit www.actionmodulers.com or contact

[email protected] for updated license fees.

http://www.actionmodulers.com/

mailto:[email protected]



2.6 Starting MOHID Studio

To start MOHID Studio, please select All Programs -> Action Modulers -> MOHID

Studio -> MOHID Studio (see Figure 2-1).

Figure 2-1: Execute MOHID Studio

2.7 Main Window

MOHID Studio’s main window is shown in Figure 2-2. On the top of the main window

the main menu is placed. Inside the client area different dockable windows are located.

The “Explorer” window (currently shown in Figure 2-2) allows managing simulations.

The “Map” window (hidden in Figure 2-2) shows the content of the GIS engine.



Figure 2-2: MOHID Studio’s main window

Beside the “Explorer” window and the “Map” window (that are always open) other

windows may appear in the client area of the main window (for example: XY Graphs,

Tools, Reports, etc.).

2.7.1 Dockable Windows

Windows inside the client area are “dockable”. This means that the user can arrange

them as needed. Figure 2-3 shows MOHID Studio’s main window where the “Explorer”

window and the “Map” window are docked side by side.



Figure 2-3: MOHID Studio’s main window (side by side docking)

To change the dock state of a window, double click on the title bar (this turns the

window floating). Then drag it to the desired position.

2.7.2 Main Menu

The main menu is divided into 9 different tabs and works in a similar way as the menu

of Microsoft Office 2007. Each tab contains a ribbon menu, organized in groups, with

several items for a specific task. As example Figure 2-4 shows the ribbon menu related

to the Map window. Each menu is explained in detail in this guide.

Figure 2-4: Example of a Ribbon Menu (Map)

2.8 Home menu

The Home ribbon menu (see Figure 2-5) is the first menu displayed by MOHID Studio

and helps you to getting started with the application. This menu is divided in three

distinct groups: Workspace, Getting Started with MOHID and Links. The workspace



group allows to use workspaces very quick (learn how to use workspaces in subsection

2.10).

Figure 2-5: Home menu

The group “Getting Started with MOHID” has some examples to introduce you to

MOHID Studio application. These examples allow importing sample solutions and

sample unit tests for a better understanding of MOHID Studio. These samples contain

basic examples helping you to create your own solutions and projects (for more

information read subsection 2.9).

The Links group contains a variety of links where it is possible to find some help with

the MOHID community.

2.9 Getting Started with MOHID Studio

The best way to getting start working with MOHID Studio is to load a sample solution.

On the group “Getting Started with MOHID”, from menu Home (see Figure 2-5), there

are two sample solutions (one MOHID Water [blue] and other of MOHID Land

[yellow]) and two samples of unit tests (one of MOHID Water and one of MOHID

Land). MOHID Studio solutions are always represented by a color corresponding to the

type of model for an easy way to work. The color blues stand for MOHID Water

solutions, the color yellow stands for MOHID land solutions and the color red stands for

MOHID River solutions.

The sample solution is loaded to MOHID Studio by pressing one of the sample

solutions button and everything is ready to run, letting you easily explore all the features

of MOHID Studio. The sample solution loaded can be changed or modified according

with your needs. It also can be saved, replacing the original sample solution. So, the

next time the sample solution button is pressed on “Getting Started with MOHID” from

menu Home (see Figure 2-5), the sample solution saved will be prompted with all the

opened layers. Although the original sample solution was replaced, it is always possible



to restore it again. The original sample solution can be restore executing simple three

steps:

1 – Delete the workspace associated to the sample solution on Workspace

Manager (on the group “Workspace”, from menu Home (see Figure 2-5));

2 – Delete the sample solution saved on Solution Manager (on the group

“Solution”, from menu Project (see Figure 3-1) – for more information read section

3.1.3 );

3 – Delete the projects from the sample solution on Project Manager (on the

group “Domain”, from menu Project (see Figure 3-1) – for more information read

section 3.2.4).

MOHID Studio help can always be found in this user guide, in MOHID Studio tutorials,

on internet forums or by e-mail. It is possible to export your solution and then request

for Professional Help (to see how to export solution check subsection 3.1.4) through the

option “Request Support”.

2.10 Workspaces

2.10.1 Introduction to Workspaces

Workspaces allow storing the state of MOHID Studio between two consecutive work

sessions. For this the workspace keeps track of the current open solution (see section

3.1) and loaded layers (see section 4).

2.10.2 Working with Workspaces

MOHID Studio does not have an explicit way to create a workspace. After MOHID

Studio finished starting, it immediately asks for the workspace to use. You might select

an empty workspace or load an existing one, as shown in Figure 2-6.


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Figure 2-6: Create a new workspace or load an existing one

When MOHID Studio exits it will always ask if the user wants to save the current

workspace, as shown in Figure 2-7.

Figure 2-7: Save workspace on program exit

Workspaces can be changed or saved at any time during a session. To open a workspace

(or create a new one) press Open in “Workspace” group from menu Home (see Figure



2-5Figure 2-5), to save the current workspace press button Save in “Workspace from the

Home menu (see Figure 2-5).

2.10.3 Managing Workspaces

Managing workspaces involves renaming and deleting existing workspaces. This can be

done by selecting Workspace -> Manage from the menu “Home” (see Figure 2-5). The

workspace manager will appear (like the one on Figure 2-8) and the user can easily

manage your MOHID Studio Workspaces.

Figure 2-8: Managing Workspaces

There are only two restrictions when managing Workspaces:

Names of workspaces must be unique;

The workspace currently opened cannot be removed.



3 Project Management

MOHID Studio organizes projects by dividing them into three major units: (i) solutions,

(ii) domains and (iii) simulations.2

A solution is the topmost unit and groups together one or more domains. For each

workspace, only one solution can be opened by MOHID Studio.

A domain is characterized by a geographic region which is covered (through the Digital

Terrain Model), the type of numerical model to use (MOHID Water, MOHID Land or

MOHID River) and the physical path on the disk where files are stored. Each domain

belongs to one or more solutions and contains a set of simulations. In the case of

MOHID Water, nested domains can be created.

A simulation is one execution of the numerical model over a given period of time. All

files (input files and result files) related with the execution also belong to the

simulation.

Projects can be managed from the “Project” menu (see Figure 3-1).

Figure 3-1: Project menu

Data associated with projects is displayed in the “Explorer” window (see Figure 3-2).

This window is divided into three main areas: (i) the Project Tree on the left, (ii) the

Modules window in the middle and (iii) the File Editor on the right.

2 MOHID GUI had a similar structure. The correspondence from MOHID GUI to MOHID Studio is:

Solution = Project; Simulation = Domain and Run = Simulation



Figure 3-2: Explorer window

The Project Tree shows the hierarchical structure of projects. In Figure 3-2 a solution

called “OpenMI Implementation” is shown. This solution contains two domains: (i)

Sample Estuary and (ii) Sample Catchment. The domain Sample Estuary shows two

simulations, ReferenceRun and Sim#2.

Some functions which can be accessed from the “Project” menu can also be accessed

from the context menu (by clicking on the right mouse button) accessible from the

Project Tree (see Figure 3-3).



Figure 3-3: Accessing project management options from the context menu

3.1 Solution

3.1.1 Creating or opening solutions

A new solution can be created by selecting Solution -> New from the “Project” menu

(see Figure 3-1) and an existing solution can be opened by selecting Solution -> Open.

A window like shown in Figure 3-4 will be shown.

When creating a new solution, a name of the solution must be provided.

Figure 3-4: Creating a new solution

When a new solution is created or opened, the current solution opened in MOHID

Studio will be closed. Note that the solution of the current workspace will be replaced

by the new solution opened or created. To prevent unwanted results, save the workspace

before open or create the new solution.



3.1.2 Closing solutions

Solutions can be closed by selected Solution -> Close from the “Project” menu (see

Figure 3-1).

3.1.3 Managing solutions

There are several tasks which can be performed with solutions: (i) rename, (ii) delete,

(iii) import and (iv) export. All these tasks can be performed by selecting Solution –>

Manage from the “Project” menu (see Figure 3-1).

Figure 3-5: Managing solutions

To change the name of a solution, use the “Rename” button. Any new name can be

given, with the exception that solution names must be unique.

To remove a solution, use the “Remove” button. Any solution can be removed, except

the currently opened solution. When a solution is removed, domains associated to the

solution are NOT removed. All domains remain available in the Domain Manage (for

more information read subsection 3.2.4).

3.1.4 Exporting solutions

Exporting a solution allows to store all information about the solution, including all

domains and data files, in a single ZIP file. This is useful if you want to exchange

solutions between computers or if you want to request professional help. To export a



solution, select the “Export” button from the “Managing Solution” window (see Figure

3-6). A window like the one shown in Figure 3-6 will appear.

Figure 3-6: Exporting solutions

The file name must be the “ZIP” archive to which the solution is exported. By default,

the exported ZIP archive does not include the result files (since they can be very large).

Result files are only included if the “Include Result files” options is checked. By

clicking the “Export” button the export process begins. Depending on the number and

size of files included in the solution, the process can take more or less time.

3.1.5 Importing solution

To import a solution select the “Import” button from the “Managing Solution” window

(see Figure 3-6). A window like shown in Figure 3-7 appears.



Figure 3-7: Importing solutions

Importing solutions allows processing two types of solutions: (i) a previously exported

solution or (ii) a project from MOHID GUI.

To import a previously exported solution check the MOHID Studio option and browse

for the ZIP archive which contains the solution.

To import a MOHID GUI project check the MOHID GUI option and browse for the

MOH file of the MOHID Project.

By clicking the “Import” button the import process begins. Depending on the number

and size of files included in the solution, the process can take more or less time.

NOTE: If a solution with the same name of the solution to import already exists, the

newly imported solution is automatically renamed.

3.2 Domains

Like mentioned previously domains are characterized by a geographic region which is

covered (through the Digital Terrain Model), the type of numerical model to use

(MOHID Water, MOHID Land or MOHID River) and the physical path on the disk

where files will be stored. Each domain belongs to one or more solutions and contains a

set of simulations. In the case of MOHID Water, nested domains can be created.

3.2.1 Creating domains

New domains can be created by selecting Domain -> New from the “Project” menu

menu (see Figure 3-1). A window like shown in Figure 3-8 appears.



Figure 3-8: Creating a new domain

The information provided in the “Creating a new domain” window characterizes your

domain. The following restrictions must be fulfilled:

the domain name must be unique;

the root directory must be empty (when the domain is created or imported).

The path to the Digital Terrain Model may not be specified during domain creation (if,

for instance it hasn’t been created yet or you want to import to the \General Data\Digital

Terrain folder after the project has been created ISTO TEM SER EXPLICADO

ALGURES). It is always possible to come back to the window shown in Figure 3-8 by

accessing the domain properties.

During domain creation, MOHID Studio creates four special folders to store general

data files: (i) one root directory (General Data) and (ii) three subdirectories (Initial

Conditions, Boundary Conditions and Digital Terrain). It also creates three folders

specific for MOHID model runs: (i) data, (ii) exe and (iii) res. The directory structure

for one specific folder, after domain creation, is shown in Figure 3-9.



Figure 3-9: Directory structure for a domain

NOTE: This approach is different the one used by MOHID GUI, since there is now one

General Data folder for each domain (in MOHID GUI the General Data Folder was

shared among projects).

3.2.2 Domain properties

Domain properties can be accessed and changed by selecting Domain -> Properties

(ISTO IST AINDA NÃO ESTÁ FEITO NO CÓDIGO ) from the “Project” menu (see

Figure 3-1). The same window as shown in Figure 3-8 will appear.

NOTE: It’s not recommended to change the Root Directory of a domain after data files

and/or simulations have been added to the domain.

3.2.3 Removing domains

Domains can be removed by selecting Domain -> Remove from the “Project” menu (see

Figure 3-1). After removing a domain from a solution it continues to exit in the data

base. To delete permanently a domain use the Manage Domains options (see subsection

3.2.4).

3.2.4 Managing domains

Domains can be “managed” by selecting Domain -> Manage from the “Project” menu

(see Figure 3-1). A window like shown in Figure 3-10 will appear.



Figure 3-10: Managing Domain

Using this window is possible to create new domains, by selecting the “Add” button to

edit existing domains by selecting the “Edit” button and remove a domain by selecting

the “Remove” button. After removing a domain, MOHID Studio asks if the folders

associated to the domain are also to be removed (Figure 3-11).

By selecting “Yes” the entire directory will be permanently deleted from your hard

disk, including the structure of the domain’s Root Directory and including all files

inside that directory. Before press “Yes”, make sure that you do not have important files

inside that directory or subdirectory.

Figure 3-11: Remove Domain

3.2.5 Nested domains

Nested domains are used to run models with sub models. This feature is currently only

implemented in MOHID Water, so MOHID Studio only allows creating nested domains



for domains of the type “MOHID Water”. The process of creating nested domains is the

same as for root domains, with the exception that the “father” domain must be selected

in the tree view while you the new, nested, domain is created. When creating a nested

domain, MOHID Studio set the root directory for the nested domain automatically.

Figure 3-12 shows the Project Tree with an example of a nested domain (domain North

Atlantic and with the nested domain Portuguese Coast).

Figure 3-12: Project Tree showing a domain with a nested domain

3.3 Simulations

3.3.1 Creating simulations

To create a new simulation, the tree node where the simulation is to inserted must be

selected first. This node can either be a domain node or a simulation node, depending of

the option if the user wants to insert a first simulation into a domain or temporal

sequence of a previous existing simulation. After selecting the desired node, a new

simulation can be inserted by selecting Simulation -> New from the “Project” menu.

A window like shown in Figure 3-13 will appear. This window can be used to specify

the properties of the simulation: (i) name, (ii) description and (iii) modules to activate.



Figure 3-13: Creating a new simulation

Each simulation receives automatically an ID (internal identification and cannot be

changed). All files which belong to a given simulation will contain this ID at the end,

before the extension of the file. For example, the input file for the hydrodynamic

module of the simulation with ID 5 will be called “Hydrodynamic_5.dat”.

3.3.2 Simulation properties

Simulation properties can be accessed and changed by selecting Simulation ->

Properties from the “Project” menu (see Figure 3-1). The same window as shown in

Figure 3-13 will appear.

3.3.3 Root and sequential simulation

MOHID Studio distinguishes between two types of simulations: (i) sequential

simulations or (ii) root simulations.

MOHID Studio assumes that root simulations always start as “cold start” (initial

conditions are obtained from the data files) and that sequential simulations always start



as “hot start” (initial condition are obtained from the previous run). MOHID Studio

allows creating branches of simulations order to study different scenarios.

Figure 3-14 shows an example of the Project Tree after setting up the simulations for

scenarios which involve studying the combination of the following cases: (i) No

Discharge vs. With Discharge and (ii) East Wind vs. West Wind. This example shows

two root (Spin up) simulations, one for the “No Discharge” case and one for the “With

Discharge” case. For both root simulations several in time sequential simulations are

shown (Day 1 and Day 2). Branches are created (starting after the Spin Up) for the

“East Wind” and “West Wind” cases.

Figure 3-14: Project Tree showing root and sequential simulation and the usage of branches

In case of inserting a simulation which continues from a previous simulation MOHID

Studio will automatically set the start date of the newly inserted simulation to the end

date of the previous simulation and change the continues compute option in all module

data files to true.



3.3.4 Removing simulations

Simulations can be removed by selecting Simulation -> Delete from the “Project” menu

(see Figure 3-1). By doing so, the current selected simulation and all nested child

simulation will be removed.

3.3.5 Files associated to simulation

Numerical models like MOHID need data files (to read initial conditions and general

compute options) and produce result files. Each simulation has associated a set of files.

After selecting a specific simulation in the Project Tree, files associated to the selected

simulation are displayed in the Module List Views, located in the middle of the

Explorer Window. Figure 3-15 shows files associated to the selected simulation in the

Module List Views. On top are located Data Files, in the middle HDF Files and at the

bottom Time Series Files.

Figure 3-15: Files associated to simulations

Data files can be easily modified and saved by MOHID Studio (for more information

about this method read subsection 3.5).



3.3.6 Copying simulation data files

It is common for users to set up two simulations which are very similar. In this case it

can be useful to copy data files from one simulation to another. The best way to it is

following the next instructions:

Select the source simulation in the Project Tree;

Select the files to copy from the “Data Files List View”;

Press the button Simulation -> Copy from the “Project” menu;

Select the target simulation in the Project Tree;

Press the button Simulation -> Paste from the “Project” menu.

3.3.7 Cleaning simulation result files

In some circumstances it might be useful to erase all result files associated with a

specific simulation. This can be done selecting the simulation in the Project Tree and

then press the Simulation -> Clean button from the “Project” menu.

3.4 Organizing data files

Data files play a central role when running numerical simulations. Like described

previously, MOHID Studio:

creates and organizes automatically data files associated to simulations;

creates a directory structure where data files associated to domains can be

stored.

3.4.1 Data files associated to simulations

When a simulation is selected in the Project Tree, in the Module List Views the files

associated to the selected modules are displayed. Names of these files are automatically

created based on the simulation ID.



3.4.2 Data files associated to domains

Data files associated to domains (e.g. Digital Terrain, Boundary Conditions and Initial

Conditions) must be supplied by the user. These files should be stored in the General

Data directory (or any subdirectory). The directory structure of the General Data

directory is displayed in the Project Tree. When a directory is selected in the Project

Tree, the files located in this directory are displayed in the Module List Views.

NOTE: MOHID Studio considers the HDF Files has an extension *.hdf or *.hdf5 and

Time Series Files has the extension *.sr*.

From the context menu (right mouse button) of the Project Tree several tasks can be

performed:

Creating a new directory inside the General Data directory

Removing an existing directory

Create a new empty data file

Create a new time series template file

Import an existing file

Figure 3-16: Project Tree context menu to perform tasks related with the general data directory



3.5 Editing data files

Data files are edited in the File Editor, which is located at the right side of the Explorer

window (see Figure 3-17). To edit a data files, simply double click over them inside the

Data File List View. Data files will appear as tabs inside the File Editor.

Figure 3-17: File Editor with two open data files

If a data files for a given module doesn’t exist yet, MOHID Studio will create it

automatically, using a template with the most common options for the selected module.

Inside the File Editor data files have syntax highlighting based in the following rules:

Keyword are red

Keyword values are blue

Block delimiter are purple

Comment lines are green

(MOHID DATA FILES – AN OVERVIEW – reference from HERE???)

In the upper right corner of the File Editor are available a set of commands which help

to edit data files:

Find Text / Replace Text – to find / replace a specific text inside the data file

Comment / Uncomment lines



Save / Save All

Close / Close All

3.6 Executing Models

When all data files are prepared it is possible to execute simulations. MOHID Studio

provides two options to execute modules: (i) run a single simulation or (ii) schedule a

set of simulations.

3.6.1 Executing a single simulation

To execute a single simulation, just select the simulation to execute from the Project

Tree and hit the Execute Models -> Run Simulation from the “Project” menu (see

Figure 3-1). The simulation starts immediately.

3.6.2 Executing a set of simulations

A set of simulations (including nested simulations) can be executed by selecting

Execute Models -> Schedule Simulations from the “Project” menu. A window like

shown in Figure 3-18 will appear.



Figure 3-18: Scheduling a set of simulations

First it is necessary to select the root domain and then all simulations which are to be

executed.

In the case of nested domains, simulations must be paired like shown in Figure 3-19.



Figure 3-19: Scheduling nested domains

3.6.3 Simulation progress

Feedback about simulation progress appears below the Project Tree, in the “Model

Controller” window (Figure 3-20). The progress bar indicates the evolution of the

simulation.

Figure 3-20: Model Controller Window



It is possible to see the screen output from the numerical model by selecting the

“Output” button in the model controller. A window like shown in Figure 3-21 appears.

Figure 3-21: Model screen output window

The execution of the model can be interrupted by selected “Kill” from the model

controller.

When a simulation is finished, all screen output from the model is stored. It is possible

to access this information by selecting “View Last Log” from the context menu of the

Project Tree.

3.7 Visualizing results

After model execution, the list views containing HDF results and Time Series results are

updated. There are several options to visualize the results directly inside MOHID

Studio. All options can be accessed from the commands located in the upper right

corner of the list views.



3.7.1 Visualizing HDF results

HDF Files can be loaded into the GIS map engine as animated maps. There several

options to display HDF results, depending on the module. A detailed description on how

to display animated maps inside MOHID Studios can be found at section 4.

From the HDF List view it is possible to load HDF files as polygons, vectors or

lagrangian animations, using the command in the upper right corner of the list view.

Figure 3-22: HDF List View with commands

3.7.2 Visualizing Time Series results

Time Series Files can be loaded into the XY Graph engine. A detailed description on

how to display XY Graphs inside MOHID Studio can be found at section 5.

From the Time Series List view it’s possible to load Time Series files into the XY

Graph engine or edit them in the File Editor.

Figure 3-23: Time Series List View with commands



4 Map Visualization (GIS)

4.1 Introduction

MOHID Studio uses a customized Geographical Information System (GIS) to display

dynamic maps. Information which can be displayed includes raster images and vector

data. All data is presented in form of layers.

Raster images are typically used to add a background to the image and can be added

from local images and from Web Map Servers (WMS).

MOHID Studio supports different kinds of Vector data sources. Special emphasis is

given to data related to MOHID models: (i) special ASCII (and XML) files in MOHID

format and (ii) model results stored in HDF Files. Other vector data sources can also be

added, including ESRI Shapefiles and HGT files. Vector data can be displayed in

several different ways, using simple styles or theme based styles. MOHID Studio also

supports time animated vector data.

Tasks related to the map visualization can be performed from the “Map” menu (see

Figure 4-1).

Figure 4-1: Map menu

Layers are displayed in the “Map” window (see Figure 3-2). This window is divided

into two main areas: (i) the Layers List on the left and (ii) the Map Display on the right

(see Figure 3-2).



Figure 4-2: Map window

The Layers List shows the currently loaded layers of the map. At the bottom of the

Layers List is located a small tool box which allows to control the current display time

(in the case time animations are loaded). The Date & Time control is detailed explained

on subsection 4.2.

The Map Display shows the maps based on the currently loaded layers. A small set of

tools, located in the upper right corner of the Map Display, allows panning, zooming

and querying the map. At the right side of the Map Display appears the legend of the

currently loaded layers.

Some functions which can be accessed from the “Map” menu can also be accessed from

the context accessible from the Layers List (Figure 4-3).



Figure 4-3: Accessing map options from the context menu

4.2 Date & Time

The Date & Time control allows to change the date and time of a simulation, displaying

the result on the Map window. When pressing “play” (see Figure 4-4) the results from

the simulation will be played and will be displayed as an animation on the Map window.

Figure 4-4: Date & Time control

The start time and end time can be changed as well as the step between displayed times.

To change the settings press on the green clock (the button on the right of Date & Time

control – see Figure 4-4). The display time can be changed in the Current Time window

as shown on the Figure 4-5.



Figure 4-5: Current Time Window

Incomplete!?

4.3 Layers General Properties

Layers loaded into MOHID Studio’s GIS have common properties: (i) if they are to be

displayed (enabled/disabled), (ii) minimum/maximum zoom visible, and (iii) layer

name.

Enabled layers are displayed in the map on top of each other, considering the same

order as shown in the Layers Lists (The top layer in the Layers List is the topmost layer

in the Map Display). Layers can be moved up and down through the context menu or

through the buttons “Move up” or “Move Down” in group “Manage Layers” from Map

menu (see Figure 4-1). Layers can be enabled / disabled by checking / unchecking the

box in the “Visible” column in the Layers List.

Properties of a layer can be accessed by: (i) double clicking over it on the Layers List,

(ii) selecting “Properties” from context menu of the Layers List or (iii) by pressing F4.



4.4 Raster Layers

Raster layers are used to mainly to display some background in the map. MOHID

Studio supports two main types of raster layers: (i) raster collections from georeferenced

images and (ii) raster images from WMS server.

To use the Raster Layers features is necessary to have FW Tools 2.4.2 installed and

correctly configured in MOHID Studio. For more information check the MOHID Studio

– Installation Guide.

4.4.1 Raster Collections

Raster Collection are a set of georeferenced raster images which are stored on your

computer. These images can be added by selecting Background -> Raster from the Map

menu (see Figure 4-1). A window like shown in Figure 4-6 will appear to configure the

Raster Collection. Here it is possible to add or remove individual images to the raster

collection.

Figure 4-6: Adding Raster Collections



Individual raster images must be georeferenced. This means that these images are either

images which contain information about there georeference (e.g. GeoTiff) or that there

is an additional file which contains this information (ESRI world file - *.jpw).

For large raster collections, and for raster collection with different resolutions, the

option to set the minimum and maximum zoom level is particularly useful. This allows

MOHID Studio to show always in image with the appropriate resolution, without being

very memory demanding.

For example, if the Blue Marble collection3 is to be used as background image, Table 2

shows a typical configuration for minimum and maximum zoom levels.

Resolution Minimum Zoom Maximum Zoom

250m 0.0 1.0

1km 1.0 10.0

4km 10.0 30.0

16km 30.0 Infinite

Table 2: Examples for zoom levels (Blue Marble image gallery)

3 http://www.unearthedoutdoors.net/global_data/true_marble/download



Figure 4-7: Displaying a Raster Layer in MOHID Studio

4.4.2 WMS Layers

WMS layers are provided by online servers over the Internet. MOHID Studio has two

preconfigured WMS Servers: (i) Demis Map and (ii) JPL Nasa. WMS Layers can be

added by selecting Background -> WMS from the Map menu. A window like shown in

Figure 4-8 will appear. In the window it is possible to select from one of the predefined

WMS Servers or to add the name address (URL) to a user defined WMS Server. After

selecting the server, the “Get Layers” button must be pressed, in order to obtain the list

of possible WMS layers.

NOTE: There are several different WMS versions. MOHID Studio only supports WMS

versions 1.0.0, 1.1.0, 1.1.1 and 1.3.0.



Figure 4-8: Adding WMS Layer

Figure 4-9 shows an example of the WMS layer for Europe (from DEMIS map) in

MOHID Studio.



Figure 4-9: Displaying a WMS layer in MOHID Studio

4.5 MOHID ASCII Layers

MOHID ASCII layers are special layers to load files which contain simplified

information about geometries specific to the usage of MOHID Water Modelling

System. These layers include: (i) XYZ Points, (ii) Grids, (iii) Grid Data, (iv) Drainage

Network and (v) Polygons.

For example, Grid Data files are used by MOHID Water to read information about the

bathymetry.

Some tools included into MOHID Studio use information from this layer while other

tools help to create specific MOHID ASCII Files. For example, to create a bathymetry

(Grid Data File) it is necessary to load:

the base data in form of a XYZ Points layer;

information about the grid in form of a Grid Layer;

information about non compute areas in form of a polygon file.



4.5.1 XYZ Points layer

XYZ Point layers are loaded from XYZ Files (see XYZ Files) and are used as input to

create Grid Data Files. A XYZ Point layer can be added by selecting ASCII -> XYZ

Points from the “Map” menu (see Figure 4-1).

After selecting a valid XYZ file, a window like shown in Figure 4-10 appears. By

default the layer name is based on the filename, the minimum and maximum visibility

are set to “always” visible and the layer style to the default gradient style, respecting the

minimum and maximum values found in the XYZ file.

Figure 4-10: Adding a XYZ Point vector layer

Figure 4-11 shows a XYZ Point Layer in MOHID Studio.



Figure 4-11: Displaying a XYZ Point layer

4.5.2 Grid layer

Grid layers are loaded from Grid files (see subsection 10.2.5). A Grid layer can be

added by selecting ASCII -> Grid from the “Map” menu. The process of adding a Grid

layer is the same like adding a XYZ Point layer. Figure 4-12 shows a Grid Layer

showing part of a curvilinear grid.



Figure 4-12: Displaying a Grid layer

4.5.3 Grid Data layer

Grid Data layers are loaded from Grid Data files (see subsection 10.2.6). A Grid Data

layer can be added by selecting ASCII -> Grid Data from the “Map” menu (see Figure

4-1). The process of adding a Grid Data layer is the same like adding a XYZ Point

layer. Figure 4-13 shows a Grid Data Layer of the bathymetry of the Tagus Estuary.



Figure 4-13: Displaying a Grid Data layer

4.5.4 Drainage Network layer

Drainage Network layers are loaded from Drainage Network files (see subsection

10.2.7). A Drainage Network layer can be added by selecting ASCII -> Drainage

Network from the “Map” menu (see Figure 4-1). The process of adding a Drainage

Network layer is the same like adding a XYZ Point layer. Figure 4-14 shows a Drainage

Network Layer of the Trancão Watershed.



Figure 4-14: Displaying a Drainage Network layer

4.5.5 Polygons layer

Polygons layers are loaded from Polygon files. A Polygon layer can be added by

selecting ASCII -> Polygons from the “Map” menu (see Figure 4-1). The process of

adding a Polygon layer is the same like adding a XYZ Point layer. Figure 4-15 shows a

Polygon Layer representing the boundaries of a watershed.



Figure 4-15: Displaying a Polygon layer

4.6 HDF Files

MOHID uses HDF files to store information about large data sets. Within MOHID,

HDF files are primarily used to store model results, but they may also be used to

provide boundary conditions or initial conditions.

MOHID uses HDF files with some special groups / datasets, in order to store time based

and georeferenced data sets. Dataset can apply to grid based (sometimes referenced as

polygon based) datasets, vector field datasets, drainage network data sets and lagrangian

particle data sets.

4.6.1 Grid Map

HDF Grid Map layers are the most common HDF layers used in MOHID (Studio). A

HDF Grid Map layers allows to display the temporally evolution of a grid based

property based on the information stored in a single HDF file. A HDF Grid Map layer

can be added by selecting HDF -> Grid Map from the “Map” menu (see Figure 4-1).

After selecting a valid HDF file, a window like shown in Figure 4-16 will appear.

Figure 4-16: Adding a Grid Map vector layer



This window has several options related to select which and how the data is presented:

from the Feature drop down box it’s possible to select the property to represent;

from the Mapping drop down box the type of mapping (Water points or Open

points)

from “Geo Dataset” if metric (Connection X / Connection Y) or geographic

coordinates (Latitude / Longitude) are to be used

from Slice the horizontal layer (by default this property is set to the top most

layer

Other options shown in Figure 4-16 have been explained earlier in the document.

After adding a HDF Grid Map layer the time animator below the layers window gets

enabled. Using this animator it is possible to loop trough individual layers of the HDF

Grid Map.

4.6.2 Vector (Arrow) Map

HDF Vector Field layers are used in MOHID Studio to display the temporally evolution

of a vector field based on the information stored in a single HDF file. A HDF Vector

Field layer can be added by selecting HDF -> Vector Field from the “Map” menu. The

window which appear is the same as the one shown in Figure 4-16 with the only

difference that the available features which appear are vector fields (with X and Y

components). Figure 4-17 shows a Vector Map of the velocity at the Tagus Estuary

Mouth.



Figure 4-17: Displaying a Vector Map

4.6.3 Drainage Network Map

HDF Drainage Network layers are used in MOHID Studio to display the temporally

evolution of properties inside a drainage network based on the information stored in a

single HDF file. A HDF Drainage Network layer can be added by selecting HDF ->

Drainage Network from the “Map” menu. The window shown in Figure 4-16 appears.

4.6.4 Lagrangian Particle Map

HDF Lagrangian Particle layers are used in MOHID Studio to display the temporally

evolution of properties of lagrangian particle based on the information stored in a single

HDF file. A HDF Lagrangian Particle layer can be added by selecting HDF -> Particle

Field from the “Map” menu. The window shown in Figure 4-16 appears.

4.7 Other Vector Layers

Besides the MOHID specific vector data formats listed previously (MOHID ASCII

Layers and HDF Files), other vector layers can be loaded into MOHID Studio’s GIS

engine. Providers of these layers are: (i) ESRI Shapefiles, (ii) XML Geometries and (iii)

HGT Layers.



4.7.1 ESRI Shapefiles Layers

ESRI Shapefiles are widely used to store geographic data. Layers based on data from

ESRI Shapefiles can be added by selecting Vector Data -> Shapefile from the “Map”

menu (see Figure 4-1). A window like shown in Figure 4-10 appears.

4.7.2 XML Geometry Layers

XML Geometries are layers based on XML files which contain geometries stored by

MOHID Studio (see subsection 10.3). Layers based on XML Geometry files can be

added by selecting Vector Data -> XML Geometry from the “Map” menu. A window

like shown in Figure 4-10 appears.

4.7.3 HGT Layers

HGT layers are based on NASA SRTM (Shuttle Radar Topography Mission) files and

are the main source for building digital terrains for MOHID Land. HGT Layers can be

added by selecting Vector Data -> Nasa HGT from the “Map” menu. A window like

show in Figure 4-18 appears.

Figure 4-18: Adding a HGT vector layer



In this window (see Figure 4-18) it is necessary to specify the geographic region for

which the HGT layer is to be loaded: (i) the current view or (ii) the boundaries of a

given layer.

After selecting the region, the necessary HGT files are directly downloaded from

NASA’s FTP server and cached on your local computer.

NOTE: Downloading and displaying HGT layers for big areas can be time consuming

and generate a lot of internet traffic. It is recommended that you should not try to load

HGT layers that cover more than 4 square degrees once.

4.8 Monitoring Station Layers

Location of the monitoring stations stored in MOHID Studio’s database can be

displayed on the map by selecting Monitoring Stations -> Meteorological, Hydrological

or Water Quality from the “Map” menu.

4.9 Label Layers

Label layers are a special kind of layers which allows to obtain quickly information

about the numerical data which is represented by a given vector layer. Label layers can

be created be choosing “Create Label Layer” from the context menu in the label list.

Figure 4-19 shows an example of a label layer created from a vector layer.



Figure 4-19: Creating a Label layer

4.10 Moving Layers

Layers are displayed in the map on top of each other, considering the same order as

shown in the Layers Lists (The top most layer in the Layers List is the topmost layer in

the Map Display). Layers can be moved up and down through the context menu of the

Layers List or by selecting Manage Layers -> Move Up / Down from the “Map” menu.

Layers can be removed from the map selecting Manage Layers -> Remove from the

“Map” menu.

4.11 Layer Styles

Vector layers are rendered based on their current layer style. Layer styles can be

“simple” or based on the feature data which is represented. Different layer styles can be

applied to different vector layers, depending on the type of the style and type of the

layer.

Layer styles of a given layer can be accessed by selecting “Edit” in the layers properties

window. Figure 4-20 shows an example of how to access the layer style.



NOTE: Properties of a layer can be accessed by: (i) double clicking over it on the

Layers List, (ii) selecting “Properties” from context menu of the Layers List or (iii) by

pressing F4.

Figure 4-20: Editing the layer style

MOHID Studio allows creating style templates to reuse predefined layer styles.

Template styles can be applied by hitting the “Apply” button shown in Figure 4-20.

4.11.1 Simple Vector Style

A simple vector style can be applied to almost any type of vector layers. A simple

vector style renders all geometries in the same way, independent of the feature data.



Simple Vector Styles are applied by default to MOHID ASCII Polygon layers, XML

Geometry layers and ESRI Shapefile layers.

Figure 4-21 shows the window which allows configuring a simple vector style.

Depending on the geometry to be rendered, different styles are used:

Points are represented by the symbol;

Lines are drawn with the line color / width and optional and outlined with the

outline color / width optional;

Polygons are filled with the fill color, using the alpha value as transparency and

optional outlined with the outline color / width;



Figure 4-21: Configuring a simple vector style

On Figure 4-22 it is possible to see two maps but with different simple vector styles. On

the first one (top map), country borders are represented by yellow lines and cities are

represented with white markers. On the second (bottom map), countries border are

represented by black lines, the areas are filled with transparency and the cities are

represented with green markers.



Figure 4-22: Showing different simple vector styles

4.11.2 Gradient Layer Style

Gradient layer style can be applied to almost any type of vector layers. A gradient layer

styles render geometries based on the feature data, applying a gradient color scale

between a minimum and a maximum value.



Gradient Layer Styles are applied by default to MOHID Grid Data layers, HDF Grid

Map Layers, HDF Drainage Network Layers and HDF Lagrangian Layers.

The Figure 4-23 shows a window to configure a gradient layer style and the Figure 4-24

shows a grid data layer with a gradient layer style.

Figure 4-23: Configuring a gradient layer style



Figure 4-24: Showing a gradient layer style

4.11.3 Transparency Layer Style

Transparency layer style can be applied to almost of any type of vector layers. A

transparency layer style render geometries based on the feature data, applying a

transparency color scale between a minimum and a maximum value.

The Figure 4-25 shows a window to configure a gradient layer style and the Figure 4-26

shows a grid data layer with a transparency layer style.

Figure 4-25: Configuring a transparency layer style



Figure 4-26: Showing a transparency layer style

4.11.4 Classified Layer Style

Classified layer style can be applied to almost any type of vector layers. A classified

layer style renders geometries based on the feature data, applying a classified color

scheme.

Figure 4-27 shows a window to configure a classified layer style and Figure 4-28 shows

a grid data layer with a classified layer style.



Figure 4-27: Configuring a classified layer style



Figure 4-28: Showing a classified layer style

4.11.5 Arrow Layer Style

Arrow layer styles are the only type of styles which can be applied to vector fields.

Arrow layer styles render arrows with a given color. Size of arrows is based on a linear

correspondence between the minimum and maximum modulus of the vector and the

minimum and maximum pixel sizes of the arrows.

The Figure 4-29 shows a window to configure a arrow layer style and Figure 4-30

shows a vector field layer with a arrow layer style.



Figure 4-29: Configuring a arrow layer style

Figure 4-30: Showing an arrow layer style



4.11.6 Style Templates

MOHID Studio allows defining style templates for usage between different workspace.

You can define new style templates (or modify existing ones) by selecting Manage

Layers -> Style Manager from the “Map” menu (see Figure 4-1). A window like shown

in Figure 4-31 will appear. Here you can add, edit or remove style templates. Style

templates can be applied to a layer, by selecting “Apply” in the layer style properties

window (see Figure 4-20).

Figure 4-31: Managing Style Templates

4.12 Querying Data

Data displayed by vector layers can be queried and displayed in tabular form. In order to

perform a query on a given layer, it’s necessary to mark it first as “Active Query

Layer”. This can be done from the context menu of the Layers List. The current active

query layer is marked red in the Layers List. After defining the query layer, it possible

to query the data by activating the query tool from the map tool box and select a region

where to perform the query. The results of the query will be displayed in the query

result window. Figure 4-32 shows the operation of querying the map.



Figure 4-32: Querying the Map

4.13 Images

MISSING

Save images

Set up images



5 Graph Visualization

5.1 Introduction

MOHID Studio uses a customized graph engine to display time series in from of XY

Graphs. The series can be loaded directly from MOHID ASCII Time Series files or

from MOHID Studio’s database.

Tasks related with Graph Visualization can be performed from the “XY Graph” menu

(Figure 5-1).

Figure 5-1: XY Graph menu

Time Series are displayed in “XY Graph” windows (Figure 5-2). “XY Graph” window

is divided in two main areas: (i) the Series List on the left side and (ii) the Series

Display on the right side.

Figure 5-2: XY Graph window

The Series List shows the currently loaded series and the Graph Display the series

graph. A small set of tools, located in the upper right corner of the Graph Display,

allows zooming and querying the series graph.



5.2 Graph Windows

5.2.1 Introduction

Graph windows can be created by several ways: (i) opening a MOHID ASCII Time

Series File, (ii) loading a series from MOHID Studio’s database, (iii) loading a

previously saved Graph Window or (iv) opening a series from MOHID Studio’s

Explorer window.

After selecting any of these four options, the Time Series Selection window (see Figure

5-3) will appear. Through this window is possible to choose the time series that will

appear on graph (by selecting and checking them on the upper part of the window) and

to choose if they will be displayed on a new window or added to an existent one (by

choosing the option on the lower part of the window).

Figure 5-3: Time Series Selection Window



5.2.2 Create from MOHID ASCII Time Series File

A new Graph Window, using a MOHID ASCII Time Series File as initial source, can be

created by selecting Graph Window -> New (File) from the “XY Graph” menu (see

Figure 5-1). After selecting a file containing one or more time series, the Time Series

Selection Window will be shown (Figure 5-3). After selecting one or more series press

ok button and the new graph window will be created.

5.2.3 Create from MOHID Studio’s database

A new Graph Window, using a MOHID Studio’s database as initial source, can be

created by selecting Graph Window -> New (DB) from the “XY Graph” menu (see

Figure 5-1). This brings up immediately the Time Series Selection Window (Figure 5-3)

with all available series in the database. After selecting one or more series, press ok

button to create a new graph window.

5.2.4 Closing a Graph Window

A Graph Window can be closed by selecting Graph Window -> Remove from the “XY

Graph” menu (see Figure 5-1) or by simple clicking the cross in the upper right corner

of the window.

5.2.5 Saving a graph window

A graph window, including all series and associated data, can be saved by selecting

Graph Window -> Save Graph. This will save the entire graph as an XML file.

Explain better? -> Possible to use as an image? All settings will be saved….

5.2.6 Open a saved graph

A graph window can be created from a previously saved XML file by selecting Graph

Window -> Load Graph (see Figure 5-1). The graph will be displayed with all series

and settings.



5.2.7 Create from Explorer

It is also possible to create graph windows directly from MOHID model results. This

can be done by double clicking over a given Time Series file listed in the explorer

window (in Time Series Files), as shown in Figure 5-4.

Figure 5-4: Open Graph windows from Studio Explorer

Templates

5.3 Series

5.3.1 Adding Series

Series can be added, as mentioned previously, from MOHID ASCII Time Series Files

or directly from MOHID Studio’s database. The processes of adding series to an

existent Graph Window is the same as create a new window, the only change needed is

to select the option “Add to an existent graph” on Series Selection window (see Figure

5-3).



5.3.2 Removing Series

Series can be removed from a graph by selecting Series -> Remove from the “XY

Graph” menu (see Figure 5-1).

5.4 Graph Layout

MOHID Studio’s graph engine allows creating completely costumes layout of graphs,

save these layout as templates and reapply template to other graphs.

5.4.1 Series layout

Series can be individually configured from the “Series Properties” box, located below

the series list (see “XY Graph” windows on Figure 5-2).

Too short…



6 Time Series Manager

6.1 Introduction

MOHID Studio contains a set of utilities that allow creating, managing and analyzing

Time Series. All utilities related with Time Series (Monitoring Stations, Parameters,

etc.) are in the Environmental Monitoring menu (see Figure 6-1) and in the Reports

menu (see Figure 6-2).

Figure 6-1: Environmental Monitoring menu

Figure 6-2: Reports menu

6.2 Environmental Monitoring menu

All Time Series are composed by a Parameter, Monitoring Station, date and a list of

values measured or modeled.

Missing more description!?…

6.2.1 Parameters

The Parameter Manager (Figure 6-3) displays the list of all existent parameters. In this

window is possible to create new parameters, edit or remove existent parameters. The

parameters that are associated to existent Time Series cannot be removed. To remove

them, the Time Series must be removed first.



Figure 6-3: Parameters manager

The Parameters properties window (Figure 6-4) allows create new parameters or editing

existent parameters. The property “Name” is the complete name of the parameter and

the “Display name” is the name that will be displayed in all the menus or reports. The

“Display name” field cannot be empty. This is the name that will be always displayed in

Time Series, all windows and Reports. The property “Units” refers to the units of

parameter, and it can be blank and the numeric format of parameter value can be

changed in the property “Display numeric format”.

Figure 6-4: Parameters properties window



Possible numerical displays formats are represented on Table 3 (For example is used the

number 123,456789 to show the numerical formats display. For percentage is used the

number 23,45).

Type Format Example

Exponential notation E 1,234568E+002

E2 1,23E+002

Fixed-point F 123,46

F3 123,457

General G 123,456789

G4 123,5

Number N 123,46

N3 123,457

Percentage P 23,45%

P1 23,5%

Table 3: Display Numerical Formats Examples.

6.2.2 Monitoring Station

The Monitoring Station manager (see Figure 6-5) allows create, modify or remove

monitoring stations. One Monitoring Station is the place where all parameters are

measured or modeled.



Figure 6-5: Monitoring Station manager

The Monitoring Station properties window (see Figure 6-6) allow to create or editing

monitoring station details. The property “Name” refers to the monitoring station name.

This name will be the displayed name for the station in all reports and menus from

MOHID Studio. There are several station types available, such as: Air Quality,

Hydrological, Meteorological, Tide, Water Quality, Waves and Others. The Longitude

and Latitude refers to the monitoring station geographical location. It is also possible to

add a photo of the monitoring station by clicking in the “Change” button. When the

photo is empty, the button label will be “Add…”. To remove the photo, press the

remove button next to the photo.



Figure 6-6: Monitoring Station properties window

Bellow the properties of monitoring station is the list of all time series that were

measured or modeled in this monitoring station. It is possible to add more time series

(read more about the Time series in the section 6.2.3) to this monitoring station and to

modify or delete the existent time series.

6.2.3 Time Series

The Time Series Manager displays the list of all time series that exist in the MOHID

Studio database. It is possible to create new time series and edit or remove the listed

time series.



Figure 6-7: Time Series manager

To create or modify a Time Series use the Time Series properties window (see Figure

6-6) by pressing the “Add…” or “Edit” button in the Time Series manager.

The Time Series properties are: Parameter (to add new parameters check the section

6.2.1), Monitoring Station (to add new monitoring stations check the section 6.2.2) and

monitoring location (ticket the check box to use the same location as the monitoring

station), Modeled Domain and Time Series Type (surface, middle, bottom, composed,

not defined or unknown).

The Time Series Values are the values that are obtained (by a measured or a modeled

result) for a specific instance of time. These values can be created, modified, removed

or imported (for more information, see section 6.2.4). To edit any value from the time

series value list (date or value) double click on the value to edit.



Figure 6-8: Time Series properties window

6.2.4 Importing and Exporting Time Series

The Import Time Series Files windows (see Figure 6-9) allow to importing MOHID

ASCII Time Series Files (more information about this file type on the subsection 10.2)

to MOHID Studio.

The easiest way to import one time series file to MOHID Studio is to following the next

steps:

1) Choose one MOHID ASCII Time Series Files through the browse button;

2) Select the time series from file to import (if the file only has one time series, it

will appear one Time Series);

3) Choose to add to an existent Station / Time Series or Create a new station;

4) Click “import”.

To import one or more time series from the same file:

5) Choose the time series;

6) Choose the monitoring station (if a new one was created);

7) Click “import”.



Figure 6-9: Import Time Series window

If the window before the Import Time Series window was the Time Series properties

window (see Figure 6-8), when importing one MOHID ASCII Time Series Files only

the first two steps above are requested, followed by pressing the “import” button.

The Export Time Series (to ASCII) window (see Figure 6-10) displays all time series

that belongs to MOHID Studio. To export one time series to MOHID ASCII Time

Series Files, select that time series to export, choose the destination path and then press

“Export” button. To learn more about MOHID ASCII Time Series Files check

subsection 10.2.



Figure 6-10: Export Time Series window

6.2.5 Moving Time Series

Moving Time Series are Time Series that the geographic measured point may change

along the time in any direction (Latitude, Longitude and/or Depth). Each measure refers

to a specific monitoring station, although the geographic coordinates may vary.

The Moving Time Series windows (see Figure 6-11) display the list of all moving times

series that are included in MOHID Studio database. Is possible to create, edit or delete

moving time series in this window.

Figure 6-11: Moving Time Series window



The Moving Time Series properties window (see Figure 6-12) display all the

information about a determine Moving Time Series. All the information may be added

or changed in this window, just like in Time Series properties window (see Figure 6-8).

In this window is also possible to add a description about the moving time series (for

example: “Demo Moving Time Series”). It is also possible to add a short description to

the values (for example: “estimated value”, “average value”, “Error – no value”)

helping to understand the values latter, if anything goes wrong. To edit the values

double click on the value to edit.

Figure 6-12: Moving Time Series properties window

Instead of filling the Moving Time Series properties window, is possible to import a

batch of moving time series values, through an XLS File (for more information, please

read section 6.2.7).

6.2.6 Field Campaigns and Visited Points

All the data and files from the field campaigns (photos, sheets, etc.) can be organized

and stored on a special feature from MOHID Studio. The Field Campaign manager

window (see Figure 6-13) allows add, edit or remove field campaigns.



Figure 6-13: Field Campaign manager window

The Field Campaign properties window (see Figure 6-14) displays all information about

one Field Campaign. The properties of a Field Campaign are the name, the dates where

the campaign took place and some description about the campaign. It is possible to

attach any type of file to this field campaign (for example: authorization sheets, the field

campaigns schedule, itinerary, etc.). All the files attached can be viewed (opened by the

system default application) or removed. The files are attached to the MOHID Studio

database, so the path to file can be modified or the file can be removed from disk.

The Field Campaign properties windows also include the list of all visited points in this

field campaign. With this list is easier to keep the history of all visited points in every

field campaigns.



Figure 6-14: Field Campaign properties window

The Visited Points can be created by clicking in button “Add…” on the Field Campaign

properties window (see Figure 6-14) and a new window will be open, Visited Point

properties window (see Figure 6-15). In this window is possible do add some

information about the weather conditions and some more useful information. The

weather conditions are very important to analyze the results measured on a distant

future.

The Visited Point properties window also allows attach files to the visited points, such

as sheets, photos and other documents. These documents are attached to each visited

point and not to the field campaign, so is possible to have different files attach to each

visited point. The files are also stored in the MOHID Studio database, so the file

location is possible and do not interfere with MOHID Studio.



Figure 6-15: Visited Point properties window

The Visited Points can also be created, editing or removing from Visited Point manager

windows (see Figure 6-16). Visited Points are created or editing through the Visited

Point properties window (Figure 6-15).

Figure 6-16: Visited Point manager window



6.2.7 Import from XLS Files

The import feature of XLS files to MOHID Studio is very useful and simple to use.

There are three different types of importation files: simple time series, moving time

series (profile) and boat cruise. Each importation file has a different format and there is

a demo file, of each type, that is installed along with your MOHID Studio. The demo

files are located on: My Documents\Mohid Studio\Templates\Data Import.

To import time series use the template “Import – TimeSeries.xlsx” and fill the values to

import. The time series template is only used for time series: date, time and parameter

value (see an example in Figure 6-17). After filling the template file, save the file with a

different name, keeping the template as is. The XLS file should be like the example on

the Figure 6-17. If there is a missing field in the line, all the line will be ignored. If the

line is empty or if the first field is empty or missing all values above will be ignored.



Figure 6-17: Import Time Series Template

To import the time series values from XLS file to MOHID Studio use the Import Time

Series window (see Figure 6-18) from Environmental Monitoring tab in the group

“Import”. First choose the parameter, monitoring station and time series type fields for

the time series that will be imported and browse for the source XLS file. After the file is

selected MOHID Studio will display all time series values found on the imported file.

This process may take a while, depending on the quantity of values to import. The press

“Import” button to complete the importation process. This process also may take a

while, depending on the quantity of values to import.

If the file has some errors or does not follow the template file (Figure 6-17), MOHID

Studio will display the error. If the message is “No values found in file” please check if

the file is correct or if the template file is the correct type for the import window in use.



Figure 6-18: Import Time Series window

Figure 6-19: Import Boat Cruise window

When the time series results from a profile measure, and the depth field is required, the

right template to use is “Import – Profile.xlsx”. This file is very similar with the time

series import file (Figure 6-17) with an extra coordinate field: depth. The “Import –

BoatCruise.xlsx” file is used for boat cruise measures or measures that required



coordinates tracking. This template file is also similar with the others but has two extra

coordinate fields: Longitude and Latitude (see Figure 6-19).

The values imported from “Profile” and “Boat Cruise” file types will be available on the

Moving Time Series window (see Figure 6-11). To edit the imported values use the

Moving Time Series properties window (see Figure 6-12).

6.3 Reports

The Reports is one of the best ways to analyze and check all values from time series

results. There are several reports available (see Figure 6-2), that are configured through

the Report Window (see Figure 6-20) and are all fully described on the next sub-

sections.

Figure 6-20: Report Window – Parameter

The Report Window is composed by two sections: the report settings content (on the

left) and the generated report content (on the right) as showed on the Figure 6-20. The

bottom of left window (see Figure 6-21) is always composed by three sections:

Settings of selected report;

Time Interval;

Output.



Figure 6-21: Report Window – Settings

The settings of selected report change in every report and will be described on the next

subsections.

The “Time Interval” (see Figure 6-21) allows the user to limit the results to a certain

time interval (for example: one day, one month, etc). If the box apply filter is not

checked, all values will be displayed.

The “Output” (see Figure 6-21) is the way to configure how the report will be displayed.

The report can be displayed on the right window of the Report window (as show on

Figure 6-20), PDF format or XLS format. For the last two formats, a location file and

name file are required. After pressing “Generate” button the report will be displayed on

window or saved in a file.

When a generated report is displaying on the Report window, the top bar of the

generated report content allows several features, such as: navigate through the generated

file report, print the report, save the report file as XLS format or/and PDF format, zoom

it and setting the page layout.

6.3.1 Report by Parameter

Reports by parameter, as the name say, are to generate reports based on parameter

values. This type of reports will show all values from a determine parameter, from all

monitoring stations. As an example, on the Figure 6-22 is a sample of a time series

values report by parameter, for the parameter “Temperature” with the Time Interval



from 01-01-2010 to 01-10-2010. The values are displayed alphabetical by monitoring

station name and by chronological date.

Figure 6-22: Report by Parameter

6.3.2 Report by Time Series

Reports by Time Series display all values for a parameter obtained (measured or

modeled) from one monitoring station. The list of parameters is displayed on the field

“Parameter”. After the “Parameter” is chosen, the list of time series displays all time

series available for that parameter. Choose the times series for the report, by selecting

the name. If there are measured and modeled parameters, it is possible to choose

between the two different types. To generate the report press the “Generate” button.

The values from Report by Time Series (see Figure 6-23) are displayed in chronological

time.



Figure 6-23: Report Window – Time Series

6.3.3 Report by Monitoring Station

The reports by Monitoring Station display all results from all parameters measured or

modeled for one monitoring station. To generate a report by Monitoring Station, select

the monitoring station on the settings panel and press “Generate” (see Figure 6-24). The

generated report will displayed the parameter, date and time, value and parameter units,

all order by chronological date.



Figure 6-24: Report Window – Monitoring Station

6.3.4 Report by Min/Max Values

The Reports by Min/Max Values generate reports displaying the minimum and

maximum values obtained (measured/modeled) from a specific Monitoring Station.

These values are separated by types of time series (surface, middle, bottom, etc), being

displayed the minimum and maximum for each other (see Figure 6-25).

To generate the Reports by Min/Max Values choose one parameter from the drop down

box, select the monitoring station from the monitoring station list and press “Generate”

button.



Figure 6-25: Report Window – Min/Max Values

6.3.5 Report by Moving Time Series

The Moving Time Series reports list all the values from the profiles measured on a

specific monitoring station. To generate this report, chose a parameter, a monitoring

station and then the date and of the first measure from that station. The Moving Time

Series Report window (see Figure 6-26) is only available when are moving time series

on the MOHID Studio database. The only parameters and monitoring stations displayed

are the ones that have values for moving time series.

The moving time series has as header the information about the station and the

parameter and the body contains the date, the depth and the value, order chronological.



Figure 6-26: Report Window – Moving Time Series

The moving time series imported by XLS files from “Profile” import and “Boat Cruise”

import may be displayed by the Moving Time Series Reports.



7 Tools

7.1 Introduction

MOHID Studio contains a set of tools. The majority of these tools works interactively

over the Map Visualization and provides the possibility to generate MOHID specific

data files.

MOHID Studio Tools can be accessed from the “Tool” menu (see Figure 7-1).

Figure 7-1: Tool menu

MOHID Studio tools are divided into: (i) geometry layers creation, (ii) grid creation,

(iii) grid data tools, (iv) watershed tools, (v) time series tools, (vi) HDF tools and (vii)

boxes tools.

Since tools work interactively over the map, some tools require creating one or more

temporary layers. These layers are added when the tool is started and removed when the

tool is closed.

Since tools work interactively over the map, MOHID Studio does not allow more than

one tool to be used simultaneously.

All tools are explained in detail next.

7.2 Geometry Layer Tools

7.2.1 Introduction

Geometry layers tools allow creating geometries interactively over the map. Normally,

geometries created with this tools, are used afterwards by other tools (e.g. points can be

used to create time series locations, polygons to define non compute areas, etc.).



7.2.2 Named Points

The Named Points tool allows creating XML Geometry file with points. This tool can

be activated by selecting Geometry Layers -> Named Points from the “Tool” menu (see

Figure 7-1). The tool appears docked on the right side of the main window as shown in

Figure 7-2.

Figure 7-2: Creating Named Points

Using this tool it is possible to create a list of points. Points can be added to the list by

selecting the “Draw” button and afterwards click on the map. After clicking on the map,

the list of points is updated. Point locations and names can be edited by double clicking

over the list shown under “Defined Points”. The current list can be saved by selecting

the “Save button”.

7.2.3 Named Lines

The Named Lines tool allows creating XML Geometry file with lines. This tool can be

activated by selecting Geometry Layers -> Named Lines from the “Tool” menu (see


Figure 7-3.



Figure 7-3: Creating Named Lines

Using this tool it is possible to create a list of lines. Lines can be added to the list by

selecting the “Draw” button and afterwards click on the map. Each click adds a vertex

to the line. The line is ended by double clicking the last point. Line names can be edited

by double clicking over the list shown under “Defined Lines”. The current list can be

saved by selecting the “Save button”.

7.2.4 Named Polygons

The Named Polygons tool allows creating XML Geometry file with polygons. This tool

can be activated by selecting Geometry Layers -> Named Polygons from the “Tool”

menu (see Figure 7-1). The tool appears docked on the right side of the main window as

shown in Figure 7-4.



Figure 7-4: Creating Named Polygons

Using this tool it is possible to create a list of polygons. Polygons can be added to the

list by selecting the “Draw” button and afterwards click on the map. Each click adds a

vertex to the polygon. The polygon is closed by double clicking the last point. Polygon

names can be edited by double clicking over the list shown under “Defined Polygons”.

The current list can be saved by selecting the “Save button”.

7.2.5 XYZ Points

The XYZ Points tool allows creating MOHID ASCII XYZ file with points. This tool

can be activated by selecting Geometry Layers -> XYZ Points from the “Tool” menu

(see Figure 7-1). It works in the same way as the “Named Points” tool.

7.3 Grid Tools

7.3.1 Introduction

Grid tools allow creating grids interactively over the map and to refine existing grids for

nested models.



7.3.2 Constant Grid

Constant grids can be created by selecting Grid -> Constant Grid from the “Tool” menu

(see Figure 7-1). The tool appears docked on the right side of the main window as


Figure 7-5: Creating Constant Grid

It is possible to select the grid origin (lower left corner) using the pick button or by

introducing manually the coordinates.

The number of columns and rows can be set in the JUB and IUB fields, respectively.

The horizontal and vertical grid step can be set in the dX and dY fields and the grid

angle in the Angle field. The “Coordinates” box allows selecting the grid coordinates

(MOHID internal format). Recommended options are:

4 for geographic coordinates

5 for metric (local) coordinates

After changing any options the grid can be visualized by selecting the “Refresh” button.

The Grid is saved as MOHID ASCII file by selecting the “Save” button.



7.3.3 Variable Spaced Grid

Variable spaced grids can be created by selecting Grid -> Variable Grid from the “Tool”

menu (see Figure 7-1). The tool appears docked on the right side of the main window as


Figure 7-6: Creating Variable Grid

It is possible to select the grid origin (lower left corner) using the pick button or by

introducing manually the coordinates.

The variable spacing is set in the XX and YY fields. Here accumulated values (starting

at zero), for the grid edges must be specified. It’s recommended to use an application

like Microsoft Office Excel to generate the XX and YY values.

Other options work in the same way as for the constant spaced grid.

7.3.4 Refine Grid

Text missing



7.4 Grid Data Tools

7.4.1 Introduction

Grid Data tools allow creating and modifying MOHID Grid Data Files. MOHID Grid

Data are used to provide MOHID data on a per grid cell basis (e.g. bathymetry,

topography, etc).

Using MOHID Studio’s Grid Data Tools, grid data can be created from a set of points

or a set of polygons.

7.4.2 Creating Grid Data from Points

Grid Data can be created from a set of points by selecting Grid Data -> Create from the

“Tool” menu (see Figure 7-1). This tool is typically used to create the digital terrain

model for the MOHID Water (bathymetry) and MOHID Land (topography) models.

Creating a Grid Data from points requires: (i) a grid on which the grid data will be

based, (ii) base data (points) which will be used to fill the grid data and (iii) polygons

which define non-compute areas (optional).

The tool appears docked on the right side of the main window as shown in Figure 7-7.


A c t i o n M o d u l e r s - w w w . a c t i o n m o d u l e r s . c o m 1 0 0

Figure 7-7: Creating a Grid Data from Points

Under the “Select Grid” option the desired grid can be chosen. The non-compute areas

can be defined by selecting the “Pick” button and click over the map on the polygon

which defines a non-compute area. Several polygons can be selected.

The base information can be either XYZ Data or HGT layers. Multiply sources can be

selected. The interpolation option allows choosing the desired interpolation method.

After selecting the filename for the final grid data, the process button activates the

interpolation process. For large data sets or large grids, the interpolation process might

take a while. Through the progress bar is possible to analyze the process status.

7.4.3 Creating Grid Data from Shapefiles

Grid Data can be created from a set of points by selecting Grid Data -> Create SHP

from the “Tool” menu (see Figure 7-1). This tool is typically used to create files which

contain information about land use, vegetation or soil types for the MOHID Land

model.

Creating a Grid Data from ESRI Shapefiles requires: (i) a Grid Data on which the grid

data will be based (Non compute areas will remain the same as in the base grid data and

(ii) a Shapefile with polygons data. The tool appears docked on the right side of the

main window as shown in Figure 7-8.



Figure 7-8: Creating a Grid Data from Shapefile (Polygons)

After selecting the base Grid Data and the source Shapefile, it is necessary to select the

feature (e.g. land cover code) on which the value mapping is to be performed. After

selecting the desired feature, the analyze button must be pressed, in order to obtain a list

of distinguish features (e.g. forest, urban areas) in the shapefile. For each feature, a

value which will be assigned to the corresponding grid cells must be provided. These

values can be saved or loaded by using the Load / Save buttons.

After filling the Value Mapping, the Grid Data file can be created using the process

button.

7.4.4 Modifying a Grid Data

Grid Data can be modified by selecting Grid Data -> Modify from the “Tool” menu (see


Figure 7-9.



Figure 7-9: Modifying a Grid Data

After selecting the Grid Data to modify under the “Select Grid Data” option, it is

possible to select the grid cells to modify over the map, using the “Pick” button. After

selecting the grid cells on the map, the selected cells get highlighted and appear in the

point list. After all points to modify have been selected, several operations can be

performed, by choosing the appropriate options in the “Math Operation” box.

Points can be transformed into “Compute Points” or “Non Compute Points” through the

“Open / Close non compute points” box.

After editing the Grid Data, changes can be persisted or discarded in the “Persist

Changes” box.

7.5 Watershed Tools

7.5.1 Introduction

Watershed tools allow preparing data files for MOHID Land. These tools include: (i)

depression removal, (ii) watershed delineation, (iii) soil depth and (iv) cross section

definition.



7.5.2 Depression Removal

MOHID Land requires a depression free digital terrain model in order to run4. After

constructing a digital terrain model (topography), the depression removal tool can be

used to remove depression from it. Depression can be removed by sink filling or by

artifact removal.

The depression removal tool can be accessed by selecting Watershed Tools -> Remove

Depressions from the “Tool” menu (see Figure 7-10)

Figure 7-10: Depression Removal Tool

The depressions removal process involves several steps. First, the digital terrain (Grid

Data) from which the depressions are to be removed must be selected and the existing

depressions must be found by using the “Analyze” button. If depressions are found, they

are highlighted on the map and listed in the “List of depressions”.

4 This applies only if the river network is to be simulated. You can run MOHID Land also in a special

mode without drainage network. In this case, the DTM may contain depressions.



Depressions listed in the “List of Depressions” can be individually removed by selecting

the up (remove by sink filling) and down (remove by artifact removal) buttons. Since

the removal of a single depression may create new depressions, the list of existing

depressions is automatically one individual depression has been removed.

Since the number of depressions can be very high, MOHID Studio includes an

algorithm to remove depressions in an iterative process. This can be done by pressing

the “Remove depressions by iterations” button. MOHID Studio will loop through all

depressions for the value of “Max. Iteration” (by default the value is 50 times).

Depressions containing less then “Max. cell filling” cells (the default value is 5) will be

removed by sink filling, others by artifact removal.

NOTE: For very narrow values or very flat areas the depression removal algorithm may

not work very well. It may be required to preprocess the digital terrain model first (for

instance with the Modify Grid Data tool).

When all depressions have been removed, the depression free Digital Terrain Model can

be saved in the “Persist Changes” box.

7.5.3 Watershed Delineation

Watershed delineation has two proposes: (i) specifying which grid cells drain to the

outlet (and as consequence distinguishing between compute points and non-compute

points) and (ii) creates the drainage network.

The watershed delineation tool can be accessed by selecting Watershed Tools ->

Delineate Basin from the “Tool” menu (see Figure 7-11). This tool requires a depression

free Digital Terrain Model.



Figure 7-11: Watershed Delineation Tool

The watershed delineation process involves several steps. First the Digital Terrain

Model must be selected from the “Select DTM” box.

NOTE: In this box appear all Grid Data layer currently loaded into MOHID Studio’s

GIS engine, so it is the user that select the right (depression free) Digital Terrain Model.

The second step is to define the area threshold value, by default is 1 ha. This area

indicates from which drained upstream area river channel are formed. The coordinates

of the outlet must also be set. They can be obtained using picking on the map.

NOTE: Watershed delineation is required in order to run MOHID Land, since MOHID

Land can only run with one single outlet. This option is optional, because it can be

useful, in a first step, to generate a drainage network for the entire digital terrain model

and only in a second step delineate the watershed, since it is easier to locate the outlet

over the entire drainage network.

In the “Output Options” box, the desired output of the delineation process is specified.

To run MOHID Land, only the drainage network is required. Information about options

used during the delineation process should also be stored, since they are required for the

Basin Geometry module (Basin Geometry check box). All other output is not required,



but may be useful for graphical visualization (namely the “Delineation” – polygon

which defines the watershed).

7.5.4 Cross Section Definition

After watershed delineation, the nodes of the drainage network do not contain cross

sections. MOHID Land needs to have the cross sections defined, in order to run. The

Cross Section Definition Tool allows defining cross sections for all nodes in a drainage

network in a simple way. This tool can be accessed by selecting Watershed Tools ->

Cross Sections from the “Tool” menu (Figure 7-12).

Figure 7-12: Cross Section Definition Tool

Cross section definition involves several steps. First the drainage network for which the

cross sections are to be defined must by selecting from the Network box (SCREEN

SHOT REVISION REQUIRED). Then the typical cross sections must be defined for,

one for each Strahler order. Cross sections are defined as trapezoidal ones (top width,

bottom width and high). It is possible to define triangular sections by setting the bottom

width to zero.

After defining cross sections for all Strahler orders of the drainage network, the

drainage network file can be saved, by selecting the save button in the “Persist

Changes” box. (SCREEN SHOT REVISION REQUIRED)



7.5.5 Soil Depth

The Soil Depth tool allows creating additional files for MOHID Land: (i) soil depth, (ii)

bottom digital terrain model (iii) slope and (iv) initial ground water level. This tool can

be accessed by selecting Watershed Tools -> Soil Depth from the “Tool” menu (see

Figure 7-13).

Figure 7-13: Soil Depth Tool

The Soil Depth tool requires a depression free Digital Terrain Model, which should be

selected in the “Select Digital Terrain” box. The parameter to construct soil depth can

be set in the “Select Parameter” box. The Min Depth and Max Depth parameter indicate

the minimum and maximum soil depths, respectively. The Max Slope parameter

indicates the maximum slope which the tool should consider. From these parameters

the soil depth is linearly interpolated considering. Grid cells with zero slopes will have

maximum soil depth and grid cell with slope greater or equal to the maximum slope will

have minimum soil depth.

The water table parameter indicates the percentage of the initial water depth, in function

to the total soil depth. A value of 0% indicates that the initial water table is close to the

bottom, a value of 50% indicates that the initial water table is at half soil depth and a



value of 100% indicates that the initial water table is closed to the top (fully saturated

soil).

In the “Persist Changes” box the target files can be selected and saved.

7.6 Time Series Tools

7.6.1 Introduction

Time series tools have two functions: (i) create files which indicate to MOHID model

the location of time series and (ii) create files which contain time series.

7.6.2 Grid Time Series Location

The Grid Time Series Location tool allows creating files which contains the grid

location of time series points. This tool can be easily accessed by selecting Time Series

Tools -> Grid Location from the “Tool” menu (Figure 7-14).

Figure 7-14: Grid Time Series Location Tool

Creating a grid time series location file involves several steps. First the grid data which

will be used as base must be selected. In a second step the locations of the grid points

must be specified. This can either be done by adding data from a Named Points layer by



selecting the points interactively over the map. The grid data location is generated by

clicking the Save button. This tool allows saving, optionally, a XML Geometry file with

the point locations. This is useful for display proposes and for later editing of the grid

time series location.

7.6.3 Node Time Series Location

The Node Time Series Location tool allows creating files which contains the node

location of time series points. This tool can be easily accessed by selecting Time Series

Tools -> Node Location. It works exactly in the same way as the Grid Time Series

Location tool.

7.6.4 Time Series from Database

The Time Series from Database tool allows extracting time series from MOHID

Studio’s database, in order to generate boundary conditions from MOHID models. This

tool can be accessed by selecting Time Series Tools -> From Database from the “Tool”

menu.

Figure 7-15: Creating a time series from the database

This tool requires that there has been previously data imported into the database (there

are several ways to import values to database, check subsections: 6.2.3, 6.2.4 or/and



6.2.7). After selecting the monitoring station, the selected series and the time window,

the MOHID Time Series ASCII file can be generated by clicking the “Save” button.

7.7 HDF File Tools

7.7.1 Introduction

HDF File tools are related to polygon based HDF Files.

7.7.2 Create from Time Series

MISSING

7.7.3 Interpolate HDF Files

The Interpolate HDF File tool allows interpolating one HDF file to a new grid. This tool

can be accessed by selecting HDF File Tools -> Interpolate from the “Tool” menu (see

Figure 7-16).

Figure 7-16: Interpolating a HDF File to a new grid

This tool requires a Digital Terrain Model and a HDF File to be loaded (“Select DTM

and Source HDF” box). The interpolation/extrapolation method is defined in the second

box. The file is being processed by clicking the “Process” button.



7.7.4 Vertical Cuts

The vertical cut tool is allows creating vertical cuts from 3D polygon based HDF File

layers. This tool can be accessed by selecting HDF File Tools -> Vertical Cuts from the

“Tool” menu (see Figure 7-17).

Figure 7-17: Creating a vertical cut from 3D HDF File

This tool requires a HDF File to be loaded. By using the “Draw” function the “Cut line”

can be drawn. The vertical cut is generated by using the “Create” button.

The instant displayed in the vertical cut, as well as the style used, is the same as in the

map.

7.8 Boxes

7.8.1 Introduction

MOHID used the concept of boxes in several ways, for example: (i) to initialize

properties, (ii) to monitor average concentrations over time or (iii) to release lagrangian

particles. MOHID Studio integrates a tool to create boxes from “Named Polygons”



7.8.2 Create Boxes

The create box tool allows creating 2D boxes from polygons. This tool can be easily

accessed by selecting Boxes -> Create Box from the “Tool” menu (as shown in Figure

7-18).

Figure 7-18: Creating a boxes file from a set of polygons

Polygons can be drawn directly over the map, using the “Draw” button. After all

polygons have been drawn, the boxes file can be saved be selecting the “Save” button.



8 File Export / Conversions

8.1 Introduction

MOHID Studio contains a set of utilities which permit to convert (or export) data from

one format to another format. All utilities address the MOHID Specific Formats (ASCII

Files, HDF Files and XML Geometries), ESRI Shapefiles and KML Files. MOHID

Studio Export / Conversion Utilities can be accessed from the “Export/Conversion”

menu (Figure 8-1).

Figure 8-1: Export / Conversions menu

All Export / Conversion Utilities are explained in detail next.

8.2 Export to KML

Export to KML utility allows exporting data to KML format. Formats which are

possible to export to KML are: HDF Polygon Files, MOHID ASCII Grid Data Files,

MOHID ASCII Drainage Network Files and Named Geometry Files. Before exporting

any data to KML, the data must be loaded as layer into MOHID Studio’s map engine.

Exported KML files can be loaded into applications like Google Earth.

8.2.1 Export HDF Polygon to KML

To export data from an HDF Polygon based layer, select Export to KML -> HDF

Polygon from the “Export/Conversion” menu. A window like the one shown in Figure

8-2 will appear. On the left side of the window, the instants to be exported must be

selected. On the left side it is possible to choose how the Z coordinate will be handled.

On the bottom you can choose where the exported files will be saved. Note that this toll

will create one KML file for each instant which will be exported. The export process is

started by clicking on the “export” button.



Figure 8-2: Export HDF to KML

8.2.2 Export Grid Data to KML

To export a Grid Data layer, select Export to KML -> Grid Data from the

“Export/Conversion” menu (see Figure 8-1). A window like the one shown in Figure

8-3 will appear. After choosing the Layer to export and the destination of the exported

file, click on “Export” button to generate the KML file.

Figure 8-3: Export Grid Data to KML



8.2.3 Export Drainage Network to KML

To export a Drainage Network layer, select Export to KML -> Drainage Network from

the “Export/Conversion” menu (see Figure 8-1) and the “Export Drainage Newtork to

KML” window will be opened (see Figure 8-4). After choosing the Layer to export and

the destination of the exported file, click on “Export” button to generate the KML file.

Figure 8-4: Export Drainage Network to KML

8.2.4 Export Named Geometry to KML

To export a Named Geometry layer, select Export to KML -> Named Geometry from

the “Export/Conversion” menu (see Figure 8-1). The window “Export Named Geometry

to KML” will be opened (see example on Figure 8-5). After choosing the Layer to

export and the destination of the exported file, click on “Export” button to generate the

KML file.

Figure 8-5: Export Named Geometry to KML



8.3 Export to ESRI Shapefile

Export to Shapefile utility allows exporting data to ESRI Shapefile format. Formats

which are possible to export to ESRI Shapefiles are: HDF Polygon Files, MOHID

ASCII Grid Data Files, MOHID ASCII Drainage Network Files and Named Geometry

Files. Before exporting any data to ESRI Shapefiles, data must be loaded as layer into

MOHID Studio’s map engine. Exported ESRI Shapefiles files can be loaded into

applications like Arc GIS.

8.3.1 Export HDF Polygon to Shapefile

To export data from an HDF Polygon based layer, select Export to Shapefile -> HDF

Polygon from the “Export/Conversion” menu (see Figure 8-1). A window like the one

shown in Figure 8-2 will appear. The process of exporting data is the same as exporting

to KML, with the only difference that no Z coordinate can be set.

8.3.2 Export Grid Data to Shapefile

To export a Grid Data layer, select Export to Shapefile -> Grid Data from the

“Export/Conversion” menu (see Figure 8-1). A window like the one shown in Figure

8-3 will appear. The process of exporting data is the similar to process of exporting to

KML.

8.3.3 Export Drainage Network to Shapefile

To export a Drainage Network layer, select Export to Shapefile -> Drainage Network

from the “Export/Conversion” menu (see Figure 8-1). A window like shown Figure 8-4

in will appear. The process of exporting data is the similar to process of exporting to

KML.

8.3.4 Export Named Geometry to Shapefile

To export a Named Geometry layer, select Export to Shapefile -> Named Geometry

from the “Export/Conversion” menu (see Figure 8-1). A window like shown Figure 8-5

in will appear. The process of exporting data is the similar to process of exporting to

KML.



8.4 Convert MOHID ASCII Geometries to XML Geometries

Conversion of MOHID ASCII Geometries to XML Geometries can be done by

selecting ASCII –> XML from the “Export/Conversions” menu (see Figure 8-1). With

this feature it is possible to convert “old” MOHID ASCII point, line and polygon files

to “new” MOHID XML Geometry files. The process of converting points, lines, and

polygons is similar.

The Figure 8-6 shows the window which allows to convert from MOHID ASCII to

XML Geometry.

Figure 8-6: Convert MOHID ASCII to XML

8.5 Convert XML Geometries to MOHID ASCII Geometries

Conversion of XML Geometries to MOHID ASCII Geometries can be done by

selecting XML -> ASCII from the “Export/Conversions” menu (see Figure 8-1). With

this feature is possible to convert “new” MOHID XML Geometry files to “old” MOHID

ASCII point, line and polygon files. The process of converting points, lines, and

polygons is similar.

The Figure 8-7 shows the window which allows the conversion from MOHID ASCII to

XML Geometry.



Figure 8-7: Convert XML to MOHID ASCII



9 Administration

In this section is explained the administration of MOHID Studio.

9.1 Introduction

The Administration menu (see Figure 9-1) is the place where it is possible to change all

types of MOHID Studio configurations. On the “License Manager” group it is possible

to register, request and validate your MOHID Studio license (for more information read

subsection 9.2).

9-1: Administration Tab

The “MOHID Studio Settings” contains several buttons to configure the basic settings

of your MOHID Studio. On the “General” setting is possible to change the paths of

MOHID executables files, output directories and some MOHID interface options. The

“Reset Database” button resets the MOHID Studio database. All the data will be

erased from your MOHID Studio database (example: monitoring stations, time series,

parameters, etc.). After reset the database, it is not possible to restore/recover the

previous database and all the data will be lost.

Through the “MOHID Studio Help” is possible to get information about your MOHID

Studio version, get help from your MOHID Studio manual and it is also possible to

request professional help for your MOHID Studio version. Help can be also found on

the internet or in our site – check “Links” group at the menu “Home” (Figure 2-5).

9.2 License Management

This subsection describes detailed all types of MOHID Studio licenses (see subsection

9.2.1), how to register and request your license of MOHID Studio (see subsection 9.2.3)

and how to validate it (see subsection 0).



9.2.1 Introduction

After installing MOHID Studio it will work for 30 days for an evaluation period.

Evaluation versions have restricted usage. In order to work with a licensed version of

MOHID Studio, the user needs to register and request a license (for more information

read MOHID Studio – Installation Guide).

There are two types of licensed MOHID Studio versions: MOHID Studio Express and

MOHID Studio Professional. Licenses are distributed on a single machine basis. Action

Modulers may provide other types of licenses upon request.

MOHID Studio Express license is free of charge and it is valid for six month period.

After this period you need buy a MOHID Studio Professional license or renew your

MOHID Studio Express license, if you want to keep using MOHID Studio Express.

MOHID Studio Express works with all features enabled, but with some restriction

(check restrictions on Table 4).

MOHID Professional Edition works without any restriction. License fees vary in

function of the requested license.

Table 4 shows an overview of all MOHID Studio licenses.

On subsection 9.2.2 is explained how to get your license and how to validate it.



Feature MOHID Studio

Express

MOHID Studio

Professional

MOHID Studio

Professional Unlimited

MOHID Studio

Professional Enterprise

Number of single machines where license can be installed

1 1 1 5

Maximum number of layers which can be displayed in the GIS engine


Maximum number of domains which can be created within a single workspace


Maximum number of scenarios which can be configured within a single workspace


Maximum number of nested domains which can be created


Maximum number of simultaneously opened XY Graph windows


Watermarks free images No Yes Yes Yes

License Period (month) 6 12 unlimited unlimited

Price (Euros) Free See note5

Table 4 : MOHID Studio License Fees (October 2010)

9.2.2 License Manager

The License Manager allows the user to request or/and validate a license. There are two

different ways to access the License Manager: through the Administration tab (see

Figure 9-1) or through the Orb button (see Figure 9-2).

5 Visit www.actionmodulers.com or contact [email protected] for updated license fees.

http://www.actionmodulers.com/




Figure 9-1: Administration Tab – License Manager

Figure 9-2: Orb button – License Manager

The License Manager window displays the type of license of your MOHID Studio

version and, if there exists, the limitations that your version has (see Figure 9-3).



Figure 9-3: License Manager – Evaluation Edition

To register and request a MOHID Studio license check subsection 9.2.3. To validate

your MOHID Studio license check subsection 0.

9.2.3 License Request

To request a license go to the License Manager (see Figure 9-3) and click on “License

Request to open the Registration form (see Figure 9-4). The fields marked with “*” are

mandatory for request a license. After filling all the fields click in one of the two

available options:

Generate e-mail with Request Code – This option will auto generate an e-mail,

by your system default e-mail client (for example, Microsoft Outlook). The

generated e-mail contains all necessary information to request one license. Just

press “send” to request your MOHID Studio license.



Generate Request Code and copy to clipboard – This option is for users that

use web mail instead of the default system e-mail client. All the information to

request a MOHID Studio license will be generated and then copied to clipboard.

Create an e-mail, with your webmail, to “[email protected]” and on

the e-mails body paste the information from clipboard. If for some reason the

user has some trouble sending the registration by e-mail, it is also possible to

contact us by fax, sending the content from clipboard.

Figure 9-4: License Request Form

9.2.4 License Emission

Estimated time for MOHID Studio Licenses:

MOHID Studio Express License – The MOHID Studio Express licenses will

be emitted within 48 hours. The license will be send by e-mail.




MOHID Studio Professional License – The MOHID Studio Professional

licenses will receive within 48 hours the detailed payment instructions. License

fee must be paid by bank transfer. Your license will be emitted and send to you

by e-mail after we received the license fee from our bank account.

9.2.5 License Validation

After receiving the e-mail with MOHID Studio license go to License Manager (see

Figure 9-3) and press “License Validation”. The License Validation is an easy process

and can be made by two different ways (see Figure 9-5).

Figure 9-5: License Validation

9.2.5.1 License Data File

This is the easiest way to validate your MOHID Studio license. The user needs to select

the option “I received the authorization file by e-mail and have saved it to disk” and

then click on the browse button (see Figure 9-5). Browse for the file



“MOHIDStudioLicense.dat” that was attached to the mail with the license. Finish the

validation process by restarting the MOHID Studio to validate the license file.

9.2.5.2 Validation Key

The user should choose the option “I received the authorization key by fax or phone and

need to validate manually” and then type the Validation Key Key (see Figure 9-6). Press

“OK” button to validate the MOHID Studio License and then browse for a place to save

the validation file “MOHIDStudioLicense.dat” (which contains the Validation Key).

Finish the validation process by restarting the MOHID Studio to apply your MOHID

Studio license.

Figure 9-6: License Validation – Validation Key

10 File Formats

10.1 Introduction

MOHID Studio have several file types and all this subsection is missing.



10.2 MOHID ASCII Files

10.2.1 Introduction

MOHID ASCII files are ASCII files which follow special formatting rules. These files

are used to provide all input information to the FORTRAN based numerical MOHID

models (MOHID Water, MOHID Land and MOHID River). Some output of these

models is also written in the format.

MOHID ASCII files are organized by keywords and information blocks, which can pile

up to three hierarchical levels and aggregate groups of keywords. This format can be

seen likewise a simple Mark-Up Language. File generation can be made manually,

using a text editor (like MOHID Studio’s Text Editor) or by tools (like MOHID Studio

Tools).

The maximum number of characters per line is restricted to 256. As each line contains

only one instruction, this restriction does not represent any practical limitation to the

user. Files can have blank lines and keywords don’t have to follow any specific order.

This reduces the effort of preparing input data files in a rigid format and reduces input

data errors. With exception to some cases, all the reading (keywords, keyword values,

blocks definition tags) are case sensitive. So caution is advised in the preparation of the

files because recognition is only achieved by full correspondence of characters in the

code and in the data files. The Figure 10-1 shows an example of a MOHID ASCII file,

with keyword, keyword values and blocks.



Figure 10-1: Example of a MOHID ASCII file

10.2.2 XYZ Files

XYZ Files are used to define a set of point with x, y and z coordinates. These files are

typically used to store information from bathymetric or topographic surveys.

XYZ Files are ASCII text file which extension should be *.xyz. XYZ Files contain a set

of blocks, each containing a set of point values. One block is delimited by the following

case sensitive keywords: <begin_xyz> and <end_xyz>.

A fourth column can be optionally included and it is handled as a character string which

can also be used as a legend for each point.

The Figure 10-2 shows an example of a three column XYZ MOHID ASCII File.



Figure 10-2: Example of MOHID ASCII XYZ file

10.2.3 Line Files

MOHID ASCII Line files are used to store simple lines. The default extension for

MOHID ASCII Line files is *.lin. This file is organized in blocks, each containing the

vertices for a determined line. One block is defined by the following keywords:

<begin_line> and <end_line>. Note that these keywords are case sensitive.

One file can contain an infinite number of blocks. Inside each block there are 2 columns

and at least 2 rows, one for each vertex of the line. The left column relates to the XX

coordinates of a point and the right one to the YY coordinates. The Figure 10-3 shows

an example of an MOHID ASCII Line file.

Figure 10-3: Example of a MOHID ASCII Line file



10.2.4 Polygon Files

MOHID ASCII Polygon files are used to store polygons. The default extension for

Polygons files is *.xy. This file is organized in blocks, each containing the vertices for a

certain polygon. One block is defined by the following keywords: <beginpolygon> and

<endpolygon>. Note that these keywords are case sensitive. One file can contain an

infinite number of blocks. Inside each block there are 2 columns: the left relates to the

XX coordinates of the polygon vertices and the right one to the YY coordinates of the

polygon vertices. The Figure 10-4 shows an example of one MOHID ASCII Polygon

file.

Figure 10-4: Example of a MOHID ASCII Polygon file

10.2.5 Grid Files

MOHID ASCII Grid files are used to stores grid. The organization of this file is divided

into a header section and a grid spacing section. MOHID supports orthogonal

horizontal grids, which can be rectangular or curvilinear. The default extension for Grid

files is *.grd. The Figure 10-5 shows examples of grids that are supported by MOHID

Studio.



Figure 10-5: Example Grids supported by MOHID

Note that in MOHID the i index refers to the YY axis and the j index to the XX axis.

For example grid cell (5, 2) is the fifth grid cell in the YY axis and the second in the XX

axis.

The header section contains information related to the grid global definitions, such as

the number of cells, the type of coordinate used, the origin coordinates of the grid, etc.

Below are shown the keywords supported in the header section of a Grid file.

ILB_IUB - Two integer numbers defining the minimum and maximum I values

along the Y-axis of the grid.

JLB_JUB - Two integer numbers defining the minimum and maximum J values

along the X-axis of the grid.

COORD_TIP - A flag which indicates the used coordinates type.

ORIGIN - Two real values, which indicate the origin of the lower left corner of

the grid.

ZONE - Integer values defining the UTM Zone where the bathymetry is located.

GRID_ANGLE - Counter-clock mesh rotation relative to the north. The base

point is the origin of the grid.

LATITUDE - Average latitude value used to compute Coriolis frequency and

solar radiation when metric coordinates cannot be converted to WGS84

geographic coordinates.

LONGITUDE - Average longitude value used to compute Coriolis frequency

and solar radiation when metric coordinates cannot be converted to WGS84

geographic coordinates.

CONSTANT_SPACING_X - Boolean defining if the spacing in the X axis is

constant



CONSTANT_SPACING_Y - Boolean defining if the spacing in the Y axis is

constant

DX - Constant spacing distance in XX axis

DY - Constant spacing distance in YY axis

If the spacing is not constant, the grid spacing section contains information about the

grid spacing in the XX and YY axis namely through defining the grid cells corners

coordinates. This information is stored in blocks, one for each direction. The data is

stored inside a block defined by the following keywords: <BeginXX> and <EndXX>

for the XX axis and <BeginYY> and <EndYY> for the YY axis. Note that the

keywords of these block definition tags are case sensitive. Each value must be stored in

a single line. The values are read from left to right corner in the XX axis and from

bottom to top in the YY axis. The first value is always zero in both directions, being the

following values cumulative. The Figure 10-6 shows an example of an MOHID ASCII

Grid file.



Figure 10-6: Example of a MOHID ASCII Grid file

NOTE: For more information about MOHID Grid files can be found here check the

following link:

http://www.mohid.com/wiki/index.php?title=Grid

10.2.6 Grid Data Files

MOHID ASCII Grid Data files relate 2D or 3D information to a grid. Grid data is stored

in an ASCII text file and has multiple and flexible formatting options. Grid Data files

are used to store one value per grid cell (for example for bathymetry, topography).

http://www.mohid.com/wiki/index.php?title=Grid



MOHID ASCII Grid Data Files contain the same section like Grid files (header section

and grid spacing section) plus an additional data section.

The data section contains the values of the Grid Data. The data is stored inside a block

defined by the following keywords: <BeginGridData2D> and <EndGridData2D>. Note

that these keywords are case sensitive. It is possible to specify the values by giving a

list of all values of all the grid cells. Each value must be stored in a single line. The

values are read from the lower left corner to the upper right corner of the grid that is

values reading is done by row-column order. The first grid data values are read in the

following order: (ILB, JLB), (ILB, JLB+1), … (ILB, JUB), (ILB+1, JLB), …, (IUB,

JUB-1), (IUB, JUB). Note that the index “i” refers to the Y-axis and the “j” index to the

X-Axis. In this case, if you have a (IUB x JUB) grid then the list must have (IUB x

JUB) values.

NOTE: More information about MOHID Grid Data files can be found on the following

link: http://www.mohid.com/wiki/index.php?title=Grid_Data

10.2.7 Drainage Network Files

MOHID ASCII Drainage Network Files are used to stores information about drainage

network. The organization of this file is divided into blocks defining single nodes and

blocks of defining links between nodes.

Single node blocks contain information related to each node which makes part of the

drainage network. Single nodes blocks are delimited by the <BeginNode> and

<EndNode> blocks.

http://www.mohid.com/wiki/index.php?title=Grid_Data



Figure 10-7: Example Node Definition

Links between nodes are defined by blocks delimited by <BeginReach> and

<EndReach> blocks.

Figure 10-8: Example Reach Definition

Due to the complexity of these files, it is recommended to generate these files with

MOHID Studio’s Watershed delineation tool.

NOTE: More information about MOHID Drainage Network files can be found on the

following link: http://www.mohid.com/wiki/index.php?title=Drainage_network

10.2.8 Time Series Files

MOHID ASCII Time series files are used to store information varying in time. These

files serve as input and as output for the MOHID numerical programs. MOHID ASCII

Time Series files should contains have an extension *.sr* (e.g. *.srh, *.srm, etc).

Time Series files have a header section containing general definition about the series

(location, time units, and name) and data section.

The header section must define the following keywords:

NAME – Name of the Station to which the series belong;

COORD_X – X Coordinate of the station;

COORD_Y – Y Coordinate of the station;

SERIES_INITIAL_DATA - definition of the series initial data;

TIME_UNITS – Time units in which the data is given;

The data section is defined inside a block defined by the tags <BeginTimeSerie> and

<EndTimeSerie>. Inside the block data is formatted into columns separated by blank

spaces. The leftmost column defines the accumulated time, in the time units defined in

the header section and starting from the time series initial date, also defined in the

http://www.mohid.com/wiki/index.php?title=Drainage_network



header section. The number of columns is limited by the default number of characters

allowed in one single line, which are 256. In order to read the properties (e.g.

temperature, salinity, wind speed, etc) associated to a certain column, a header line must

be present on the line just above the <BeginTimeSerie> tag. The number of properties

names in this header line must be equal to the number of columns in the data section

including the accumulated time column. The names must be separated by blank spaces,

thus properties names with blank spaces are not allowed. Blank spaces of properties

must be replaced by an underscore. The Figure 10-9 shows an example of a simple time

series file with one column and in the Figure 10-10 it is possible to see an advanced

example.

Figure 10-9: Example MOHID ASCII Time Series file (simple)



Figure 10-10: Example MOHID ASCII Time Series File (advanced)

10.3 XML Files

10.3.1 Introduction

MOHID Studio uses XML files to store data of many kinds. Many of these files are for

internal use only and are not described here. XML Files suitable to be edited are XML

files which contain geometry information. These are described along the next

subsections.

10.3.2 XML Named Points Files

XML named points files are used to store “named points” and can be generated with

MOHID Studio’s tools. An example of a XML Named point file is shown in Figure

10-11.



Figure 10-11: A XML Named Point File

10.3.3 XML Named Lines Files

XML named lines files are used to store “named lines” and can be generated with

MOHID Studio’s tools. An example of a XML Named Line file is shown in Figure

10-12.

MISSING IMAGE

Figure 10-12: A XML Named Line File



10.3.4 XML Named Polygon Files

XML named polygon files are used to store “named polygons” and can be generated

with MOHID Studio’s tools. An example of a XML Named Polygon file is shown in

Figure 10-13.

MISSING IMAGE

Figure 10-13: A XML Named Polygon File

10.4 Other Formats

10.4.1 HDF Files

HDF5 is a general purpose library and file format for storing scientific data. It is the

standard input/output format of spatial and/or temporal data sets in MOHID. Through

MOHID Studio’s integrated map engine it is possible to visualize data contained in

HDF files. Besides this, MOHID Studio includes tools to manipulate HDF Files and

export data from HDF files to other formats.

HDF5 itself does not define a standard of how to georeference data sets, nor how to

time reference data sets. In order to overcome this lack of definition, MOHID defines

some special rules how data inside a HDF file should be organized, in order to be

MOHID-HDF. For more information about this subject can be found at the following

link: http://www.mohid.com/wiki/index.php?title=HDF_file

MOHID’s modules produce HDF files which contain: (i) polygon (grid data) based data

sets, (ii) drainage network based information and (iii) lagrangian (particle) based data

sets.

http://www.mohid.com/wiki/index.php?title=HDF_file



10.4.2 ESRI Shapefiles

The ESRI Shapefile is a popular geospatial vector data format for geographic

information systems software. It is developed and regulated by ESRI as a (mostly) open

specification for data interoperability among ESRI and other software products.

MOHID Studio is able to disable data contained in ESRI Shapefiles. Some MOHID

Studio tools are based on ESRI Shapefiles and through file conversion it is possible to

convert between ERSI Shapefiles and other file formats.