2023-001 Qimera MBES POP REV01

2023-001
QIMERA MULTIBEAM PROCESSING
Ocean Winds NY Bight 0537
Bluepoint Wind Project
GEO-SERVICES
www.acteon.com
1. PURPOSE
The purpose of this document is to provide direction for MBES processing using Qimera with data collected in Qinsy.
This document is project specific to 2023-001 adhering to the latest revision of TS-QM-GL-001 Guideline for Control of
Governing Documents. For specific project amendments, the Project Manager is responsible for scheduling and enlisting
this document owner’s assistance and approval for the content and procedure of the amendment.
2. ABBREVIATIONS & DEFINITIONS

ABBREVIATIONS
MBES Multibeam Echo Sounder
DEFINITIONS
N/A xxx
3. CODE, STANDARDS & REFERENCE MATERIAL

DOCUMENT NO. TITLE
Company References
Xxx xxx xxx or N/A Xxx
Industry Standards and Specifications
IHO S-44, S100
3rd Party References

xxx
4. ROLES & RESPONSIBILITIES

The designee listed on the title page is responsible for the issue and maintenance of this document. All TerraSond Em-
ployees and contractors are required to follow this Guideline and any project specific amendments approved by this
document’s owner or designee.
The Executive Management Team is responsible to ensure their staff use this document to create and manage governing
documents by following this guideline.
TERRASOND - CONFIDENTIAL AND PROPRIETARY

The contents of this material are confidential and proprietary to TerraSond and should not be reproduced, published, or disclosed to
others without express authorization of TerraSond.
5. QIMERA MULTIBEAM ECHOSOUNDER (MBES) DATA
PROCESSING SOP
This SOP provides the required steps to follow when processing MBES data. The SOP is tailored to the processor who
receives the data first from the acquisition team regardless of whether the processor is located onshore or offshore.
For processors receiving data that has already been partially processed and organized into the respective projects, the
workflow will be slightly different and will be tailored to skip a few of the initial steps (1 through 6) but will require the
processor to verify that these steps have been undertaken by using a combination of the processing line logs and the
actual Qimera projects before continuing with the rest of the workflow.
Images within this document are from different versions of Qimera. Slight variations in screen shots could be due to a
processor using a newer version, but the utility remains applicable.
This SOP should be used together with the Navigation processing SOP for POSPac and the MBES data processing logs.
The Project Execution Plan (PEP) will provide the project specific guidelines related to expected survey quality, data
specifications and deliverables for the survey.

Table of Contents
1 Workflow Overview. .................................................................................................................................. 3
2 Data Management ..................................................................................................................................... 4
3 Detailed processing Guide. ........................................................................................................................ 5
3.1 Step 1: Project setup and update ........................................................................................................................... 5
3.1.1 Step 1A - Create or Open Qimera Project. ...................................................................................................... 5
3.1.2 STEP 1B - Configure Shortcuts......................................................................................................................... 6
3.1.3 STEP 1C - Load Raw data files ......................................................................................................................... 8
3.2 Step 2: Check, Verify and Updated vessel settings. .............................................................................................. 12
3.3 Step 3: Creating and updating surfaces ................................................................................................................ 15
3.3.1 Create a Dynamic and Static Surface ............................................................................................................ 15
3.3.2 Update a Dynamic Surface ............................................................................................................................ 17
3.4 Step 4: Sound Velocity Profile Check .................................................................................................................... 18
3.5 Step 5: Importing Post Processed Navigation, Delayed Heave, and Tide ............................................................. 21
3.5.1 SBET and RMS ............................................................................................................................................... 21
3.5.2 Importing Tide Files....................................................................................................................................... 26
3.5.3 Importing Delayed Heave ............................................................................................................................. 30
3.6 Step 6: Vertical Referencing Method .................................................................................................................... 32
3.6.1 RTK (Accurate Height) ................................................................................................................................... 32
3.6.2 Tide (unreliable height) ................................................................................................................................. 34
3.7 Step 7: Inspecting, Cleaning and Editing Data in Qimera ..................................................................................... 42
3.7.1 Editors ........................................................................................................................................................... 42
3.7.2 Beam Blocking ............................................................................................................................................... 48
3.7.3 Filters............................................................................................................................................................. 49
3.7.4 Vertical Shift Tools ........................................................................................................................................ 59
3.7.5 Tide Tool........................................................................................................................................................ 67
3.7.6 TU Delft Sound Speed Inversion Tool ........................................................................................................... 69
3.8 Step 8: Data QA/QC Tools ..................................................................................................................................... 71
3.8.1 Time Series Editor ......................................................................................................................................... 71
3.8.2 Sounding Density .......................................................................................................................................... 71
3.8.3 Cast Shadows ................................................................................................................................................ 73
3.8.4 THU and TVU Surfaces .................................................................................................................................. 75
3.8.5 Coverage ....................................................................................................................................................... 76
3.8.6 Cross Check Analysis ..................................................................................................................................... 80
3.8.7 Surface Difference Tool ................................................................................................................................. 83
3.8.8 Profile and Ruler Tool.................................................................................................................................... 87
3.9 Step 9: Exporting ................................................................................................................................................... 88
3.9.1 XYZ ................................................................................................................................................................. 88
3.9.2 GSFs ............................................................................................................................................................... 93
4 Processing a Patch Test ............................................................................................................................ 95
4.1 ROLL ...................................................................................................................................................................... 96
4.2 PITCH ..................................................................................................................................................................... 98
4.3 YAW/HEADING .................................................................................................................................................... 100
5 Troubleshooting ..................................................................................................................................... 102
5.1.1 Wobble Tool ................................................................................................................................................ 102

1. WORKFLOW OVERVIEW.
1. Load Raw Data: Create a project to load data into or add data to an existing project. Use acquisition log to ensure
that all acquired data is loaded into the right project.
2. Check Vessel settings: Verify vessel settings by checking transducer offsets, patch angle corrections, uncertainty
Values, the draft, and HADR. Update these values if needed and notify acquisition team so that the changes are
made in Qinsy.
3. Create dynamic surface and static surface to view the loaded data.
4. Check and Apply Sound Velocity Profiles (SVPs).
a. Ensure SVPs are loaded in from DB (Use the SVP acquisition log), otherwise import the SVPs directly into
Qimera.
b. Set the SVP selection strategy in the Sound Velocity tab of the Processing Settings Editor.
i. Start with Nearest in Distance within Time: 120 minutes.
ii. Can increase time as needed or change selection method.
5. Import Navigation and Tide data.
a. Load SBET and RMS (See the POSPac processing guide for SBET and RMS generation). Ensure that the
corresponding RMS file (smrmsg.out) is in the same folder as the SBET.
i. Create appropriately labeled position and motion objects into which the SBET data will be loaded.
ii. Select the co-ordinate system in which the SBET was exported.
iii. Select the start date (Sunday) of the week in which the data was acquired.
iv. Enter the uncertainty values from POSPac Processing Log. Note that these static values will only
be used if Qimera can not locate the RMS file with real the time RMS values.
v. Load SBET Motion but set POS MV Motion as priority in the Motion Source Priorities of the Position,
Motion, Heading tab of the Processing Settings Editor.
b. Load tide files. Verify the tide data by checking the datum and time format. Tide file should have only two
columns: YYYY/MM/DD Time and Tide
c. Load delayed heave. Delayed heave is computed and stored in the raw navigation files like the 000 files
for POSMv.
6. Set the appropriate Vertical Referencing options in the Processing Settings Editor
a. For an Ellipsoid Reference Survey: Set the Vertical referencing method to RTK(Accurate Height) and then
select the appropriate Vertical Geodetic Offset method and corresponding uncertainty.
b. For a conventional survey using tide observations from tide gauge station: Set vertical Referencing Method
to Tide (unreliable height). The tide files and tide strategy should have been set up prior to this step.
7. To Clean and Edit Data use a combination of the following tools to fix any remaining artifacts in the data. The
selection of which tools you can use will be dictated by how much data coverage has been achieved in an area/
zone and the timeline for deliverables most notably the daily deliverable to the client. The processing log must be
updated with the details for each tool applied on a line-by-line basis.
a. Editors (1D,2D and 3D) for inspecting data, flagging features of interest, cleaning noise and testing filters.
b. Blocking- Can be set up to filter data according to survey order, beam number range, angle, and transducer
specific flags.
c. Run Filters – After testing in slice editor, to reject noise and to fix unresolved artifacts most notably, SV
artifacts, constant vertical busts between adjacent lines.
d. Run TU Delft Sound Speed Inversion tool when several lines have an SV artifact (Smile or frown) and
overlap data from lines without any SV artifacts. This tool requires overlap between adjacent lines and
depending on the number and length of lines on which it’s applied might take a considerable processing
time.
e. Tide Tool – This tool can be used to fix small vertical busts in the SBET using the original POS data.
f. Varying vertical shift Tool - can be used to fix small varying vertical shifts between adjacent lines.
8. Complete data QC checks in line with project/client specifications on Coverage, Density, TPU, and crossline check
(when crossline data is available). The results of these checks will have to be summarized in the processing logs.
9. Export required deliverable in specified format. For offshore processing, at a minimum most clients will need a daily
deliverable showing the extent and quality of all data acquired on a survey day and a cumulative surface at specified
time interval.
2023-001_QIMERA PROCESSING GUIDE Page 3

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Return to workflow Overview
2. DATA MANAGEMENT
Good data management is key to our operation. MBES projects can contain terabytes of data that we as a company have
a legal obligation to store and secure for a lengthy period. Excessive duplicates and poor management will take up signif-
icant space on the servers. A data management plan and proper folder directories will be setup before processing. A
standard folder directory will be used, as multiple people will be looking for and using data sets.
For projects with a large survey area whose data would exceed 50 GB, blocks/zones will be established and separate
projects for each block created (after processing there needs to be QC between all projects); this will speed up computa-
tion and make cleaning and exports manageable. All Qimera projects should be backed up on the agreed upon Ter-
raSond server in accordance with the established data management plan.
• 01_XXVesselName_ProjectNumber\01_Data\02_Processing\01_NAV MBES\01_QIMERA_Projects
Processing logs are not only a requirement for most clients, but standard practice at TerraSond. The format can vary but,
should contain all processes that were applied to each line and what was exported. The format should be agreed upon
at the project level and can even be attached to or a continuation of the field acquisition log.
• 01_XXVesselName_ProjectNumber\01_Data\02_Processing\06_Processing_Logs
All columns in the logs MUST be filled out; even if something is Not Applicable (‘NA’), it should be noted as such.
There are no exceptions.

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3. DETAILED PROCESSING GUIDE.
The Qimera user guide provided by QPS can be accessed here: Getting Started - Qimera (qps.nl)
3.1 Step 1: Project setup and update

3.1.1 Step 1A - Create or Open Qimera Project.
Data can be loaded into Qimera by using already existing project or by creating a new project.
To create a new project, open Qimera (Use the project approved version if there’s more than one version installed on
the station.) and create a new project relevant to the project based on the section/area/project etc.
Existing projects that have been opened on the user’s station can also be accessed through this menu by double clicking
the project in the pre-view or using the “open other” option and navigating to the required project folder.

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1. Give the project a relevant name (Project#_VESSEL_AREA/BLOCK/etc.) and ensure the location and pro-
ject path are correct (01_XX_Project#\01_Data\02_Processing\01_NAV MBES\01_QIMERA_Projects).
Keep the project Coordinate System as “Automatic” – Qimera will automatically choose the projection
based on the source of the files being imported.
**The Qinsy project is setup with the correct coordinate transformation applied in real-time. This can be
verified in the properties of each line after it has been imported into Qimera **
3.1.2 STEP 1B - Configure Shortcuts

Qimera is very big on hot keys, which can be read about in the quick start guide at the link below. Some of the most use-
ful ones are; CTRL+F to bring up the project directory; In slice editor, while using the Fixed Slice Select, use W and S key-
board keys to move the slice forward and backward and holding shift +W/S move the entire selection area for-
ward/backward (Caps Lock On and then W or S will move the selection area); and holding Shift to easily move around in
the 3D editor and plan view while a tool is selected.
A full list of shortcuts can be accessed by from the main menu under Projects>Configure Shortcuts.

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3.1.3 STEP 1C - Load Raw data files
1. Once the new project has been created, Qimera will prompt to add raw files to the project. There are two ways
to add raw files into the project.
a. This prompt will eventually time out and disappear. If so, add raw files by going to the “Source” tab:
Source > Add Raw Sonar Files > Add Files
b. Right-click on the “Raw Sonar Files” tab in the Project Sources window on the left side of Qimera.
In the image below, the area on the left will appear blank at first: click ‘Add Files’ and navigate to the folder on the com-
puter where the DBs for the project are located (01_XX_Project#\01_Data\01_Acquisition\01_NAV MBES\09_Raw_DBs).
The box will populate with the files selected > Click OK to add the files to the project.
NOTE: ALL DBS MUST BE ADDED TO THE PROJECT. EVEN IF A FILE IS NOT GOING TO BE USED FOR THE MBES GRIDS, IT
MAY STILL REQUIRE EXPORTS FOR OTHER USES AND SHOULD ALWAYS BE IMPORTED. THESE FILES NOT USED FOR
MBES PROCESSING CAN THEN BE GROUPED AS AN “UNUSED” SET BUT MUST REMAIN INSIDE THE PROJECT.
NOTE: On import of raw data files (*.db), Qimera will create *.qpd files and store them within the project folder (ex.
Qimera_SOP_Example\ DtmData\Vessel-Name\). The *.qpd files store all the edits that are made to the raw files – this is
to ensure that the raw data is not affected during cleaning. These files can also be brought into Qimera for example, for
final gridding from multiple projects. Ensure that projects with the source .db files are never open at the same time as

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projects with the correlating .qpd files. When both projects are open, they could become corrupted, and any pro-
cessing progress lost.
2. Qimera will auto detect the vessel configuration setup in Qinsy. This must be QC’d after import, before pro-
cessing. Click OK to import files into the project, and auto process once all files loaded.
3.1.3.1 Import Troubleshooting
Qimera version 2.3.5 does not allow for the same vessel name with different objects with the file. The following import
message will appear when trying to load *.db files with the same vessel name but different configurations. This may
happen if the vessel file in Qinsy has been altered. Ask the Navigation station if this has occurred and report it to the PC.
FOR EXAMPLE, FROM SARAH BORDELON: There are now two vessel files for OWF: “Sarah_Bordelon” and “Sarah_Bor-
delon_IDH”. The naming convention change occurred when the port MBES head was swapped out. Normally, “auto de-
tect vessel configuration” is supported. If the import message above appears, copy the two files:

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• SarahBordelon_IDH.20200627_111002.vesselconfig
• SarahBordelon_IDH.20200627_111002.squattemplate
…from D:\07_Vessel_Config into the Qimera Project Folder D:\01_QIMERA_Projects\2020-004_Sarah_Bor-

delon_WTGXXX\Vessel and click the “…” near “Override Configuration” to browse to this folder and select the vessel
configuration file. Then click OK. See image below.
The following SV profile duplicate message may also appear during the import process, make a note of it, click OK. And
check the SV Editor for duplicates. This is a known issue in previous versions but should be resolved in 2.3.5.
Organize Project Sources Window…it is a good idea to organize the Project sources window after import to reaffirm the
two separate vessel files.

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3.2 Step 2: Check, Verify and Updated vessel settings.
3. To check/change the vessel configuration select all files and click Tools>Vessel Editor.
The user may notice that there are many Qinsy options/nodes that are carried over and are adjustable for processing.
a. Confirm the required settings for the Transducer (Both Port and Starboard Heads for dual head) TPU
computation are accurate (The image below provides an example, but the values should be verified for
each survey, Check with the Lead Surveyor and SME). All standard deviations entered in Qimera are 1-
sigma standard deviation. The final output is 2-sigma standard deviation in line with IHO specifications.
i. SD Roll, Pitch, Heading Offset = 0.01
ii. SD Surface Sound Speed = 0.03
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iii. Beam Width Along = 1.00
iv. Beam Width Across = 0.50
Be sure to QC both the Port and Starboard MBES Head Uncertainty.
b. Enter the draft values into the draft section of the Vessel Editor. These values should carry over from
acquisition, but at a minimum should be checked in Qimera. The draft section has 2 values that need to
be input. The Draft can be found in the acquisition log on the Measure Down tab. Be sure to enter each
draft measurement that was taken during the dates that the project covers. The Height Above Draft Ref-
erence (HADR) is the offset from the draft reference (for TerraSond this is usually MBES phase center) to
the COG, value is offset from the draft reference point to the COG positive up. If the COG is collocated
with the draft reference, leave this value as 0. This is the only way to update draft values. The DB must
be loaded into the project to take effect; this option will not update draft for any QPD (Processed Point
Files) added to the project separately. Changes to draft for QPD files needs to take place in the original
project where the raw DB was loaded/processed.

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2. Once all Systems and the associated offsets have been QC’d, draft and HADR have been entered, and Standard
Deviations (SD) have been entered correctly, save the vessel configuration.
3. Once the files have been imported/vessel file QC’d into the project they will need to be processed. Qimera will
prompt for the files to be processed; click Yes
This prompt will also eventually time out and disappear. If so, process each file by clicking on the wheel next to each in-
dividual line file or select the “Auto Process” wheel in the main menu. For those familiar with Caris, this is the SVP and
merge process where tide, sound velocity, offsets, SBETs, etc. are all being applied to the data. Qimera does all the pro-
cesses in the correct order for the user at once based off the processing setting.

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3.3 Step 3: Creating and updating surfaces
3.3.1 Create a Dynamic and Static Surface
Once each line has been processed, Qimera will prompt the processor to generate a Dynamic Surface to view the data. It
is good practice to create a static surface before completing any cleaning or filtering for comparison to the final data.
A. To create a dynamic surface,
1. Select all lines desired in the surface under the “Raw Sonar Files” in the Project Sources window.
2. Then click on the “Create Dynamic Surface” quick button in the menu tabs.
3. A Create Dynamic Surface window will open in which you can name the surface appropriately, set
the preferred cell resolution and select the desired processing settings as shown below.
4. Click OK. The Dynamic Surface will now appear in the Project Layers tab under “Dynamic Surfaces”
as shown in the image below.
5. When the dynamic surface is selected, Qimera provides options to view different Depth Layers
(Shallow, Deep, Average and CUBE), and color each of these layers by various properties including
Height, Uncertainty (95% C. l.) and sounding density among others. There are options to change the
color map, shading parameters, transparency and offset (NOTE this offset control does NOT affect
the data and only changes the display order by moving a surface above or below say the line tracks).
6. Turn the dynamic surface update frequency from Always to Manual. With the dynamic surface
selected, under Update select the drop-down arrow and select Manual, read the warning, and select
Yes to change the update to Manual. This will allow you to decide when to update the dynamic
surface to reflect updates to the data files.
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B. To create a static surface (think snapshot at a given time):
1. Select the dynamic surface from which a static surface will be created under the project layers tab.
2. Select Dynamic Surface to open the Dynamic Surface options
3. Select “Snapshot as Static Surface…”
4. The Snapshot as Static Surface window opens, in which you can name the static surface
appropriately and select the layer and statistic for which the static snapshot is desired as shown
below.

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3.3.2 Update a Dynamic Surface
When the processing of the data files has been completed successfully after any of the Steps 3-6, in the Project Layers
tab, right click the dynamic surface and select Update Dynamic Surface from Edits to apply the updates made to the
data. When the update to the surface is complete, a quick comparison between the static surface created in Step 2 and
the now updated dynamic surface can be done using the profile tool.

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3.4 Step 4: Sound Velocity Profile Check
1. Sound Velocity Profiles (SVP) will be added directly into Qinsy during acquisition, immediately after each cast for
real-time ray tracing. The *.db files will contain the SVP casts embedded within them and will be imported into
Qimera when importing Raw Sonar Files. View the associated SVP casts in the SVP Editor tool, to edit any spurious
points and check that the profiles captured the full water column, have accurate time, and position, and have the
correct SD for the sensor (**Note this is very important for TPU calculations**). Make sure to check the SV for all
vessels in the project from the dropdown on the top left of the SVP Editor shown below.
2. If for any reason there are no SVP’s associated with the data (not uploaded into Qinsy) and it is necessary to load
a cast, import a cast file. There are several file types that can be imported including ASCII SVP, HYPACK SVP, Caris
SVP, and Reson SVP.
3. Go to the Source tab: Source → Import → Kongsberg ASVP File…, navigate to the folder location where the SVPs
are stored.

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4. Select the SVP cast (*.asvp file) to import and open it. An “Add Kongsberg SVP” window will pop-up. Ensure that
the correct vessel is selected. Click OK.
5. Click OK and apply the SVP cast in the Processing Settings Editor.
6. There is additional SVP information that can be added manually under the processing settings editors tab .
This allows you to pick an SVP that is closest to a particular line/lines within distance and time. It is a good rule of
thumb to apply this to all lines at the beginning of the project.
a. Select all lines the SVP will be applied to and then select the Processing Settings Editors icon to open
the Processing Settings Editor Window.
b. In the Sound Velocity tab, the default Qimera setting will be “specific sound velocity profile.” Depending
on the job other settings may be preferred. Often used is “Nearest in distance, within time.” Adjust the

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time to match the frequency of the SVP acquisition in the field, make sure the selected time window is
not much smaller than the time between SVP casts.
c. Hit apply and OK. Once this is done, all affected files that need to be processed will be indicated by the
symbol . Depending on the project size, this can take a long time so try to apply all edits in one batch.

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3.5 Step 5: Importing Post Processed Navigation, Delayed Heave, and Tide
The processor should know the reduction method through which measured depths will be referenced to the project
vertical datum. This has already been decided for every project. For an ellipsoid reference survey follow section 3.5.1
and for a traditional tide survey follow sections 3.5.3and 3.5.2 below.
3.5.1 Importing SBET and RMS

For details on creating SBET data in POSPac MMS, please see POSPac Processing SOP. SBET and RMS files are created when
there is a post processed navigation solution that constrains the positional and motion solutions for the data.
** Ideally, wait at least 41 hours from the time of data acquisition before processing the Navigation data in POSPac to
generate an SBET. This allows the use of the IGS Rapid solution for the GPS Satellite Ephemerides. However, the client’s
requirement for daily deliverables will require SBETs to be processed 12-24 hours after data is acquired before some of
the IGS Rapid solutions are available. **
Ensure that SBET file and RMS file are in the same folder and have the same name that includes “sbet” and “smrmsg” in
the respective file names e.g., Year_JulianDay_Vessel_Project-ID_sbet/smrmsg.out
SBET file name: 2021_322_SS_2021-023_sbet.out
RMS file name: 2021_322_SS_2021-023_smrmsg.out
1. Once an SBET is generated, load the SBET file by going to the Source tab and selecting “Add Binary Navigation
Files”: Source → Add Binary Navigation Files. Be sure to select the proper vessel for the import of these files if
there are multiple vessels and vessel configurations.

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2. An “Import Navigation” window will pop-up; update the “Position System Reference” and “Motion System
Reference” data. Click on the button under Position System Reference and fill in the Name (e.g.,
SBET_POSN_JD###). Horizonal and Vertical Uncertainty (SD 63%) from the SBET Processing tab of the logs should
be entered, this will only be used by Qimera if the corresponding RMS file is not detected by Qimera.
3. Click on the button under Motion System Reference and fill in the Name. For Position System Reference,
name it as “SBET_POSN_JD###,” and for Motion System Reference, name it “SBET_MOTN_JD###.” Verify that all
the default Uncertainty settings match the quoted manufacturer accuracy for the motion sensor being used. If
there are multiple times or segments of SBETs, add the time or segment to this name as well.

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4. Ensure that the Position, Height, Motion, and Heading boxes are checked as shown below and that the Acquisition
Date Reference is correct. Qimera will automatically select this, and is usually correct; however, this should be
confirmed (if the wrong week is chosen, the file will not process correctly). Note that this date is based on GPS
Week, which is the Sunday of every week.
5. Ensure that the right SBET origin coordinate system is selected. For most projects, the SBETs are exported in the
native WGS84 from POSPac which ensures that all transformations are completed in QPS software, Qinsy during
acquisition and Qimera during SBET import. This is not always the case as the transformation can be completed in
POSPac. Therefore, it’s important to know and select the correct SBET co-ordinate system (a note will be to the
SBET processing log).

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6. Click OK, and after the Qimera completes the SBET extraction process, verify that the matching RMS file has
been found by Qimera in the Job Activity tab as shown below, by displaying a message” Info: Found matching
RMS file: XXX_smrmsg.out” between the start and end SBET extraction messages.
7. Since TPU is recomputed during the raytracing step (which is done in full line reprocessing), ignore the prompt
Qimera will give at the top of the screen to adjust the navigation to the lines covered by the SBET. DO NOT CLICK
YES ON THE PROMPT. This only applies the new navigation data to the lines and is NOT a full raytraced solution
and WILL NOT UPDATE THE TPU with the SBET SD or .smrmsg values.

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8. Instead, select the lines with the reprocess symbol next to them and then click the reprocess symbol on the
top toolbar. To verify what reprocessing needs to occur, hover mouse over line to see what will be processed.
9. Once the SBET is fully loaded and applied to the lines in Qimera, click on the processing settings editor to QC that
the file is being appropriately applied in Qimera to the sources for position, motion, heading and RTK referencing
methods. If any of the four applications do not appear as available, you may have to remove the file and re-add
the binary navigation file. The reprocess button signifies that a change has been made.
10. For projects where the Patch was processed without SBETs applied, ensure that Raw POS is set to the primary for
motion. If this is not set properly there will be a noticeable tilt in the data.
**QPS recommends using the raw, POS Motion in processing and this step should be followed. During
import of the SBET, follow the steps above and load in the SBET motion so that it exists within the
project. However, in the processing settings, the POSMV Motion should be made the only priority by
unchecking all JD SBET Motion and bringing the POSMV Motion to the top of the list. This should also
be done when processing a patch test to ensure the optimal offsets are calculated using the proper
motion input.**

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11. To double check which uncertainty values that were applied to an SBET, navigate to the Vessel Editor, select the
SBET Position in question, and select the uncertainty icon at the top. The horizontal and vertical SD will be
shown in a new pop-up window, as shown below. If these values are incorrect / do not match the log values,
please correct them.
3.5.2 Importing Tide Files

This section highlights the steps required to use tide gauge data reduce observed depths during a survey. For surveys
within the United States, tide data can be downloaded from the NOAA website (https://tidesandcurrents.noaa.gov/sta-
tions.html?type=Water+Levels) and used for vertical referencing. Before this data can be imported into Qimera, it must
be formatted into two columns:
a) yyyy/mm/dd Time
b) Verified (m)
Due to how the data is structured when downloaded from the NOAA website you will need to combine the date and
time into one column using the following formula in excel:
concatenate(text(A2,“yyyy/mm/dd")&" "&text(B2,"hh:mm:ss"))
1) To add Tide Files, navigate to Source and select Add Tide Files. You will be prompted to select the file configura-
tion. Ensure there are only 2 columns, with the first being Date and Time, and the second set to Numeric. If the
software is having difficulty reading the format, verify that the dropdowns for Data Type is set to Date/Time,

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then Numeric, and the Use As is set to Time and Tide. If not set correctly the software will not recognize the
ASCII files format.

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2) Before the Tide File can be imported, the tide gauge station details must be added. On the Add Tide File window
select Add Station and input the relevant information. It is good practice to include the stations name as well as
its unique ID as stated on the NOAA website.
3) Once the Tide File has been imported, it will appear either under Processing Setting Editor → Vertical Referenc-
ing and under the Project Sources window. Please note that when using a tide file, Delayed Heave will need to
be imported as shown below in section 3.5.3

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3.5.3 Importing Delayed Heave
This step is not required. It is at the discretion of the PC, Leads, and MBES Processors to determine if Delayed Heave
should be applied for data improvement. However, it is most likely not to be applied.
Delayed Heave (generically known as Delayed Heave) is the Applanix (or other heave sensor) filtered heave solution
produced automatically by the POSMV using a backward-looking filter (averaging over the prior 3 minutes of heave data).
The Delayed Heave is stored in the .000 files logged by the POS and does not require post processing.
1. Select the lines to load Delayed Heave into. Choose Source → Add Binary Navigation Files.
2. Select all POS files in the file name sequence (i.e. .000, .001, .002 … .XXX)
** Note: To load in all the POS files at one time, the files must all be in the same GPS week, as shown in the
message below. If any POS files in a sequence span the GPS week rollover (Sunday 00:00 UTC), the segments that
started before the rollover will need to be imported separately from those after the week rollover. **
3. Click on the button under Motion System Reference and fill in the Name. Leave all other settings as the default
settings.
4. Ensure that the DELAYED HEAVE box is checked as shown below. Lastly, ensure that the Acquisition Date
Reference is correct – Qimera will automatically select this, and is usually correct, however confirm this. Note that
this date is based on GPS Week which is the first Sunday of every week.

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5. Once the Delayed Heave data is loaded, select the affected lines, and hit the afore mentioned auto-process icon.

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3.6 Step 6: Vertical Referencing Method
3.6.1 RTK (Accurate Height)

For ellipsoid referenced surveys, to reduce the data to a tidal datum, a vertical geodetic offset in the form of a separation
model or a static value needs to be added and correctly applied.
1. Select all files and go to the Project Settings by clicking on the “Processing Settings Editor” symbol , or select
the file(s) of interest and right click to select Edit Processing Parameters.
2. In the Vertical Referencing tab, select RTK (Accurate Height) in the Vertical Referencing Method options box and
verify that the most accurate navigation solution is being used which the SBET solution.

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3. Separation (SEP) values (model or static value) will be needed with the correct Standard Deviation (SD).
4. The separation model is already created by the office; however, instructions for the creation of an *.sd file can be
found here: (https://confluence.qps.nl/qimera/latest/en/how-to-qimera-create-an-sd-model-for-geoid-
separations-152153511.html).
5. Check “Separation Model”, navigate to the location of separation model *.sd file and select it. Next change the SD
to the standard deviation of the model (e.g., 0.0991m).
The separation model *.sd file can be loaded as a background image (Layer>Add Fledermaus SD…) to verify that
the survey area is completely with the extents of the separation model.
** Note: If not in the project’s datum, it will prompt to transform the surface. Click Yes. Then Apply the Separation
Model. Qimera will prompt to update the Dynamic Surface. **

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3.6.2 Tide (unreliable height)
For conventional surveys, to reduce the data to a tidal datum, tide data and delayed heave data needs to be loaded as
shown in sections 3.5.2 and 3.5.3.
1) In the Vertical Referencing tab, select Tide (unreliable Height) in the Vertical Referencing Method options box
and ensure that the delayed heave source has been loaded and is checked.
2) After the Tide File has been imported, create a Tide Strategy. This will allow you to put in specific corrections for
the tide station being used in relation to the location of your survey site to allow for a more accurate vertical
reference.
a) To create a Tide Strategy in Qimera, right-click on Tides under Project Sources and select Create Tide Strat-
egy.

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b) For this method, leave as Single Station unless multiple stations are being used in your survey area. The val-
ues for this section can be found using this online interactive map ArcGIS - CO-OPS Regional Zoning . Time
Offset is listed as Average Time Correction, referring to average high and low tide, Tide Offset is a vertical
offset that would be selected at the discretion of your SME, and Tide Scale is listed as Range Ratio, which is a
multiplier used to scale the tidal values.

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c) Applying a Tide Strategy within bounds
If the survey area crosses between the boundaries of multiple tide zones, the tide zone boundaries will need
be defined for each zone separately as part of the strategy.
i. To define the zone boundaries for a Tide Strategy, select “polygonal area” and “import points”. The
shape boundary must be an ASCII to be imported into the Tide Strategy.
ii. The following steps show an example of how to extract the tide zone boundary co-ordinates from a
shape file in global mapper.
a. In Global Mapper, after importing a shapefile of the regional tide zones as well as a GeoTIFF of
your working surface (to ensure you are selecting the correct zone), right-click on the shapefile
and select Edit Attributes.

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b. With the Attributes Editor open, click on the zone that contains your surface. This will cause the
associated data in the Attribute Editor to become highlighted.
c. Right-click on the associated row and select Copy the Selected Features to the Clipboard.

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d. Press CTRL + V and this will prompt you to select which layer to copy the data to. Select “Create
New Layer to Paste to” so it will be an independent surface.
e. This will create a new layer in your Control Center. Right-click on it and navigate to Layer then
Export Layer(s) to New File…

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f. The required export format is Text File. Once that is selected, leave the ASCII Export Options set
to default.
g. Once exported, return to the Tide Strategy Properties window to import the file. Select Import
Points on the lower right of the window, choose Import from ASCII File… and navigate to the
desired file.

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h. To ensure that the strategy was applied in the polygon, compare the surface with a static sur-
face where the strategy was applied throughout. These two surfaces should come into align-
ment when crossing into the polygon that was used as the strategy bounds.

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3.7 Step 7: Inspecting, Cleaning and Editing Data in Qimera
3.7.1 Editors
3.7.1.1 Swath Editor, 1D
Another cleaning tool is the Swath Editor; this tool allows cleaning of soundings directly from individual processed raw
files, rather than several swaths like the Slice Editor.
1. Select the individual line to edit and press the Launch Swath Editor button. Navigate to the Swath Editor
through the menus at the bottom of the project:
2. The same tools described in the Slice Editor section are used in this editor.
3.7.1.2 Slice Editor, 2D
After the correct filtering level has been applied, manual cleaning might be required and can be done with the Slice Editor.
1. Select the Fixed Slice Select tool and draw a box around an area of the Dynamic Surface to edit.
2. Open the Slice Editor by selecting the button. To scroll through the Fixed Slice Editor, press “W” to Walk
forward, and “S” to Step backwards.

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3. To toggle between different color option for each swath, left click and hold on the small color bar in the Slice
editor window.

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4. Scroll through the “Slices” to view the 2D profile for noise / outliers. There are several tools (shapes) available to
use, be sure to choose the Red Square to remove (The green square is to accept data, and the blue is to select
with multiple options by right clicking on the selected area).
Below are some examples of what noise / outliers should be cleaned:

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5. To change which lines / how many lines to view / edit in the Slice Editor click the down arrow in the upper right
corner to view 1) Edit Only Selected Files, or 2) Show Unselected Files or show or hide reject soundings.

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3.7.1.3 Slice Editor, 3D
1. Select the Fixed Slice Select tool and draw a box around an area of the Dynamic Surface to edit.
2. Open the 3D Slice Editor by selecting the button. To scroll through the Fixed 3D Slice Editor, press “W” to
Walk forward, and “S” to Step backwards.
3. Scroll through the “Slices” to view the 2D profile for noise / outliers. The same tools (shapes) as the 2D editor are
available. This editor can show a different perspective in dynamic areas, that aren’t captured in 2D.

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3.7.2 Beam Blocking
Various projects require that an IHO survey order is met. A TPU blocking filter will reject soundings that do not meet the
defined specification.
**NOTE: If the TU Delft Tool is to be used for sound velocity correction (the static surface should indicate if this is needed),
apply the TPU filter AFTER TU DELFT HAS BEEN RUN to remove any refraction from the line. There is a risk of cutting out
large sections of outer beams if the line has not been corrected for refraction first. **
Remember to set filters for both the port and starboard heads for a dual head transducer.
1. Open the Processing Settings Editor using the button and go to Blocking. If a dual head system, be sure to
use the drop down next to system to select which head the blocking will be for. Normally this will be done for
both heads.
2. Check the box for TPU and chose what limit (Horizontal and Vertical) and Standard (User defined and follow TPU
specifications calculated in the processing log OR select the IHO S-44 5e survey Order required for the project.
3. Brightness and Collinearity (quality flags for Reson MBES sensors) filters are also a good way to clean out any
large/obvious noise. If these were on during acquisition, they will already be checked and filtered. To bring the
soundings back they just need to be un-checked. Note that this flag may not be available for transducers from
other manufacturers.

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3.7.3 Filters
**Starting in Qimera 2.3.1, the filter menu bar on the top of the Qimera screen only allows the application of a filter to
all lines or to data within a set boundary. To apply filters to a single line or specific set of lines, the filter must be selected
from the drop down at the top menu and then the user must check and highlight only the lines they want to filter in the
Project Sources. Right click the lines and select “Run Sounding Filter on Files…”
It’s good practice to test out the desired filter in slice editor to get an idea how the filter works before applying it to the
entire line.
Each processing station may have different filters available. All stations will have the standard filters made by Qimera,
within the red box below, but then each processor can have their own custom filters. Steps on where to find custom
filters and how to create them can be found in 3.7.3.2

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3.7.3.1 Qimera Inbuilt Filters
In Qimera, there are inbuilt filters that can be used. We often use the Spline Filter. A Spline Filter is a good, quick way to
remove noise from the Dynamic Surface. The Spline Filter does more or less the same as a data processor would do man-
ually: it attempts to determine what the bottom, or a feature on the bottom, is by fitting a surface spline through the
noisy footprint data and filter out any footprints that lie far away from this surface. This is done in two passes:
1. The first pass will filter large blunders to create a well-fitting surface spline.
2. A second pass will filter noise.
There are 5 Spline Filters that can be applied from Very Weak Spline to Very Strong Spline, where Very Strong Spline is
the most aggressive filter. Spline filters are related to IHO Order levels of cleaning. A strong filter is IHO Order 1. Very
Strong is Special Order. Use these with caution and QC immediately after application. The filter may reject sand waves
or other data features. If this happens use a weaker filter.
1. Ensure that the Dynamic Surface is selected and go to the menu tabs and select the Spline Filter to run.
2. Select to run the filter on the All Files or within a boundary from the top menu or run the filter on
Selected Files by right clicking on a selected set (mentioned above). The Dynamic Surface will update after this
Filter has been applied.
Before weak Spline After weak Spline
** Note: Compare the Dynamic Surface with the Static Surface made earlier to ensure the spline filter did not
remove wanted data. For example: around shipwrecks or sharp bottom features such as sand waves.

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3. Filters can be undone by reverting the filter for all or selected lines. It can also be useful to test the filter in slice
editor to determine if it will get the desired result. If it does not give the desired result, all one must do it select
the undo error in slice editor, thereby preventing a surface update and reverting any other filters that have been
applied.

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3.7.3.2 Custom Filters
Qimera has the option to use the standard filters in addition to custom filters. Below are some examples of the most
common custom filters used in processing. To see what custom filters are already on the station, select the filter drop
down and see the list beneath “Custom Profiles.”
To create or edit the custom profiles, select “Manage Filter Profiles” to open a window where existing custom filters can
be adjusted, and new filters are created.

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As mentioned earlier in this section, always test a filter in slice editor first to verify the desired result. If settings need to
be altered, refer to the “manage filter profiles” window to make the needed corrections.
Below are three examples of custom filters commonly used. Refer to the details tab under the “add filter operation”
window to learn more about the settings for each.

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3.7.3.3 Spot Editing Techniques and Hints
If the MBES is tuned well and there are not many environmental factors affecting the data, along with good SVP
distribution (temporal and spatial), then the Spline filter will do a good job at removing the bulk of the noise but doesn’t
get it all. This is also where computing Cast Shadows is helpful in seeing noise that needs to be cleaned out.
1. To locate the soundings the spline misses, change the Depth Layer to Shallow. This will help shoal based data be
most visible.
2. Open the Shading Parameters and increase the Vert. Scale and change the Lighting direction to bring out point
features. Setting the Altitude to 50 as opposed to 45 will make features more prominent.

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3. Pan through the surface, looking for jumps in colour or pixels that jump out. To move the box displayed in slice
editor, Alt + click on the next area to move the box with more ease.
4. Using the Slice Editor tool , draw a box around the suspect area, , turn on the Slice Editor.

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Examples of areas that need to be looked at:
5. After all the data has been scanned over, using the Shallow setting, change it to Deep setting and repeat.
Examples of Deep areas that need to be looked at.
Changing the colour scale will help to make them more visible. Another tip is to only select the area of concern
and edit the smallest possible edit. It will greatly increase the speed of the process and the regeneration of the
surface.
6. Now change the colour map to midwater.cmap by left clicking on the dropdown and choosing load colormap.
7. Color by Uncertainty 95% CI.

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8. Now look for areas that are green to red. They will indicate a higher uncertainty and possibly point out noise
9. Another option is to create a dynamic surface with Cast Shadows enabled, as discussed in Step 9 and Step 10
above. Remember, enabling the Cast Shadows will slow down processing speeds.

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3.7.4 Vertical Shift Tools
In Qimera there are multiple kinds of vertical shift tools. We use the Varying Vertical Shift and Line Height Matching
Tools most often. These tools can be found under Tools → Dynamic Surface Shifts
3.7.4.1 Varying Vertical Shift
There can be instances when the Tide Tool does not address vertical issues in the surface and Varying Vertical Shift is a
better option. By using a surface difference, a vertical shift is applied by computing the time-varying vertical offset
between two surfaces. For optimal results, there needs to be overlap on both sides of the line to be shifted with the rest
of the surface. In addition, this line and the surrounding data needs preliminary cleaning. If there are fliers in the data,
the result of the varying vertical shift will be less accurate and give a less desirable result.
**NOTE: Like TU Delft Tool, results will vary depending on the amount of overlap. Therefore, it is up to the processor to
decide if it is best to apply the VVS tool before or after trimming beams. More data is desirable but noisy data may give a
bad result. **
To use the Varying Vertical Shift tool, follow these steps to ensure that the tool shows an improvement to the data.
1. Take a screen shot of the surface prior to the shift. Select an image that represents the worst offset between the
selected line and the rest of the data.

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2. Create a Dynamic surface of ONLY the line that you wish to apply Varying Vertical Shift to. Then remove that line
from the surface you wish to match it to. Take a second screenshot of the same profile between the surface of
the one line to be shifted and the surface containing other adjacent lines.
*** For this tool to work, the line to be shifted cannot be included in both surfaces. ***
3. Now that you have two surfaces, you are ready to apply Varying Vertical Shift. Go to Tools→ Dynamic Surface
Shifts→ Varying Vertical Shift Tool.
a. For “Dynamic Surface to Shift” Select the surface of the single line you wish to shift.
b. For “Reference Surface” Select the original surface with the one line to shift removed.

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***The yellow line above is the result of the Varying Vertical shift to be applied. Be sure to investigate any areas
that show a flatline. This can often be an indication of a failed result due to not enough overlap of the two
surfaces.
4. If satisfied with the result, select “Save Shift.” Ensure that the selected line is the line to have the shift applied. If
so, select “Continue” which will prompt the line to be reprocessed.
5. After the line has been reprocessed it can be added back into the original surface. Take a final screenshot to
show the shift in the line. Scan through the rest of the line to ensure that the shift gave a good result for the
whole line.

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3.7.4.2 Line Height Matching Tool
The line height matching tool can be used when there is a consistent vertical misalignment of a line or segment. It is an
automated process that calculates the offset between all neighbouring lines in an area to determine the required verti-
cal correction. This offset is based on the slice of data loaded when the tool is run. For this reason, only data with a con-
sistent vertical misalignment is recommended. Keep in mind that any line segments that have this tool applied should
have all other segments checked for their own misalignment.
1) The first step is to draw a slice over the area of interest, ideally one that represents the vertical bust present in the
whole line and where there is minimal noise.
2) Once a slice has been drawn in the appropriate area. To open the tool, go to Tools→ Dynamic Surface Shifts-> Line
Matching Tool. The control window and plot window will open as shown below.

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3) The lines that will be used for reference will be locked, while the lines that are intended to be shifted vertically will
be unlocked. To run the process once the desired lines have been unlocked, select the “Auto Compute” button.
The suggested offset will be displayed in the control window with a preview in the plot window as shown below.
4) If happy with the suggested offset, save the changes and close out of the tool. Any lines with an offset applied will
need to be reprocessed.
5) To verify the offset, or see any other vertical offsets that have been applied using these tools, go to Processing Set-
tings Editor, under the “shifts” tab. Any types of shifts that have been applied to the selected data will show a check-
box next to them.
To view a list of all shifts that can be exported as a text file, select “Review Shifts.”

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Note that when opening this tool again, any shifts that have been previously applied will be shown as zero. The control
window only shows the changes that will be made in that current session. Ensure that any previously shifted lines are
locked. If these lines are not locked, new shifts will be calculated. This will cause old work to be overwritten and lost. The
new shifts will not be cumulative.
When applying the vertical shifts (varying vertical shift and line height matching), it is necessary to know how to undo
the shifts. To remove them go to Tools → Dynamic Surface Shifts → Adjust Vertical Shifts. The window below will give
the option to remove all, or only certain types of the vertical shifts. This is recommended to do before ever applying
these shifts more than once to a line.

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3.7.5 Tide Tool
If there are artifacts like the images below caused by tidal jumps or GNSS vertical busts that negatively affect the data and
there is a secondary data set (second tide gauge or secondary GNSS), then the secondary data can be forced into use for
that small area (or change it for the whole line in the processing settings) using the tide tool.
Example: Use the tide tool to replace section of SBET with Hemisphere corrections.
1. Tools →QPS Plugins →Tide Tool)
2. Import SBET on top and Hemisphere on bottom

- hint: find the timestamp for the data with motion error and add the raw pos for that section only
3. Find the area in the SBET window
4. Click the selection tool and “delete from”
5. Select the area and click the hammer
6. Switch to match → Original and then use the hammer next to Linear Interpolate at the top.
7. If the edit is adequate, save it (but only save the section that was edited). Once it is saved add it to the project and
update the affected areas.
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3.7.6 TU Delft Sound Speed Inversion Tool
TU Delft should only be used if some files in the project have refraction artefacts that the SVP profiles do not fix (smiles
and frowns in the across track profile). TU delft will smooth these by comparing the soundings in overlapping lines (needs
15-30% overlap), then applying a harmonic sound speed to make the lines match. This is math based and can be controlled
and the inversion/iteration process refined throughout processing. The resulting harmonic sound speed corrections can
be viewed in the Time Series editor and toggled in the processing settings. **Note: Overlap is needed!!!**. The SD for the
algorithm is 0.05 m/s.
**NOTE: If the TU Delft Tool is to be used for sound velocity corrections there must be overlap on both sides of the line.
Results will differ depending on the amount of overlap. Therefore, use best judgment to run TU Delft either before or after
trimming beams. It is also very important to clean all fliers before running this tool. **
To Apply the TU Delft:
1. Look at the Uncertainty layer of the surface to identify which lines have refraction issues (lines that show
significantly higher uncertainty in the outer swath).
2. Take a 2D slice across suspect lines and confirm there is a refraction issue.
3. Select all lines that require refraction correction as well as the surface that contains them all. DO NOT SELECT
LINES THAT DO NOT NEED TU DELFT CORRECTIONS.
4. Navigate to Tools → TU Delft Sound Speed Inversion.

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5. The Quick Search option is best for a 1st pass because it takes much less time than the Full search. Use Course for
the same reason. (If the Quick search does not produce satisfactory results, try re-running with Full Search or
Coarse Configuration and adjusting the harmonic sound speed range).
**Note: The TU Delft process takes up almost all the computer’s CPU (>90%) and will greatly slow down any other
processes running. The user can still work on other projects when it is running but expect much slower load and
processing times.
6. Finally, re-inspect the lines and re-apply TU Delft on lines the require further correction. The user may want to
clean out noise on lines that did not find a good match to improve the next TU Delft correction.
** Note: An alternative to TU Delft is to apply a filter to correct the sound velocity to a specific line. **

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3.8 Step 8: Data QA/QC Tools
3.8.1 Time Series Editor
Here Primary, Secondary, Tertiary, Quaternary positioning source(s) (e.g., SBET, RTK, DGNSS, etc.) can be viewed and
inspected/edited. First, select an individual line, then navigate to the Time Series Editor window. Ensure there are no
anomalies, time gaps, etc. The user can also view X-Position, Y-Position, Heave, Surface Sound Speed, etc. and do a multi-
plot to graph and correlate time series, for example heave, roll, and surface sound speed to diagnose heave artifacts.
3.8.2 Sounding Density
1. In Project layers, with the Dynamic surface of interest selected, the sounding density can be viewed by changing
the “Color By” to Sounding Density.
2. Next, select: Colormap→ Adjust Colormap Range, to view a histogram of the distribution of the density.
3. To determine the average Sounding Density; In the example below, the average would be ~20 pings per 0.5m. Be
sure to create the right surface resolution of surface from which to obtain and report on Density statistics. An
example is when the client wants the bathymetry data grided to 0.5m resolution and the Density reported as
pings per square meter, a new surface grided at 1m resolution will be required for reporting the density.

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3.8.3 Cast Shadows
Another useful tool that can be selected upon creation of a Dynamic Surface is the “Compute Cast Shadows” option. It
seems the default for Qimera Dynamic surface shading is Hill Shading + Cast Shadows.
These options can be changed by selecting, Project>Preferences…, to open the preferences window. In the General tab of
the preferences window, under Scene Rendering, the desired Dynamic Surface Shading option can be selected which will
in turn dictate the shading options available when creating a dynamic surface.
The images below show the options’ pairings for preferences and creating a dynamic surface. Option 1 will allow the use
to decide when to use compute Cast shadows whereas options 2 and 3 will compute the cast shadows for all new dynamic
surfaces. Option 3 (Qimera default) is the preferred option. Using Option 1 speed up the surface creation process.

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3.8.4 THU and TVU Surfaces
Once a dynamic surface has been created, THU and TVU Surfaces should be produced. Be sure to have entered the
appropriate SD in the vessel file BEFORE creating these surfaces. Since THU/TVU surfaces are created as Sd Objects,
changes made to the data or vessel file will not automatically apply to these. New surfaces will have to be created after
making any changes.
**NOTE: This is a newer feature starting in Qimera v2.1.0.
1. Select the Dynamic Surface whose THU and TVU grids are desired. Select Dynamic Surface in the main menu and
in dropdown menu, select: Create THU and TVU layers… The process will run, when complete there will be two
surfaces with the Dynamic Surface name -THU and -TVU under Sd Objects in the Project Layers Tree
2. Highlight each surface and select the colormap bar. Adjust Colormap Range to see the Max and Min for each
surface. Be sure that these meet IHO Special Order for the depth, as shown in the table below. Use the tab in the
processing log to calculate the exact THU/TVU allowances. Once these are created and reviewed, they can be used

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to aid cleaning and troubleshoot. Again, be sure SD values in the vessel file are finalized BEFORE creating these
surfaces.
Another way to approach this would be to change the layer of the Dynamic surface to shallow. This allows a look
at the minimum depths which can be used in the TPU calculator.
Water Depth Vertical Uncertainty Horizontal Uncertainty
35 – 40 m 0.39 m 2m
30 – 35 m 0.36 m 2m
25 – 30 m 0.33 m 2m
20 – 25 m 0.31 m 2m
15 – 20 m 0.29 m 2m
10 – 15 m 0.27 m 2m
5 – 10 m 0.26 m 2m
0–5m 0.25 m 2m
3.8.5 Coverage
Most surveys require 100% coverage at a minimum. This means that consecutive lines should not have any data gaps
between them, and no holidays should exist on the overall grids at the specified cell resolution.
If a boundary shape file is available, this should be imported (Layer>Import ArcGIS Shape…) into Qimera to ensure that
there are no gaps between outer most data line and the boundary line.
Any holidays or areas of concern for the proper overlap should be noted and addressed to the Lead and DC immediately
for rerun.
An easy tool for checking for holidays can be found in Global Mapper. Load in either the GeoTIFF or XYZ surface, right
click on the surface and navigate to Layer > BBOX/COVERAGES. Be sure the layer that needs the coverage polygon cre-
ated is checked. Then, select No – Create Polygonal Coverage Areas.

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The resulting coverage polygon can be exported as a shapefile from GM and used in Qimera to identify holidays and
overall coverage. Once exported, bring the coverage shapefile into Qimera to see if additional data can be added to fill
any holidays.

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3.8.6 Cross Check Analysis
Cross Check Analyses should be performed when available as an additional data QC method. Cross Check requires at
least two valid, processed, or raw sonar files or processed points files and one Dynamic or Static surface to run. Simply
select the line or lines to be used to compute the statistics and the surface to perform the statistics on.
1. Hold Ctrl and click only the cross lines in the map view or the project sources tab as shown below. Be sure that
the surface does not contain both main lines and crosslines that are being analysed. There should be a separate
surface for main lines as well as a surface for cross lines.
2. Once cross lines and the mainline surface are selected, navigate to Tools → Cross Check Tool… The process will
run, and the progress will be shown by the progress bar in the lower left corner of the Cross Check Window.

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3. Once the analysis completes, select the appropriate Statistics Specification (Special Order) and review the plots
and statistical results to see if the test passed.

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Several options for exporting these results exist from the top right corner of the Cross Check window drop down,
including ASCII Statistics, Plot Images, etc. These can be exported to include in the QC Reports and logs.

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3.8.7 Surface Difference Tool
Another good method for both crossline analysis and comparing adjacent projects is the Surface Difference Tool. This
tool creates a surface based on the difference in the overlap of two surfaces.
Once there are two surfaces that need to be compared for alignment, go to Layer→Surface Difference
1. The first window requires the selection of the first surface.
2. The second window requires the selection of the second surface fir the difference operation.

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3. Select the order of surfaces to be compared and the Data. Often, all data will be used for the surface difference.
Then select the constraints. If polygon is selected, please note that the polygon file must be an ASCII file.

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4. Select “Finish” when all options are appropriately set. Only select this command once. It takes longer than
expected for the result to compute. When it is finished, a window will appear prompting a location to save the
surface.
5. Save a screenshot of the Surface Statistics window display. Make note of the values, especially the Mean,
Median, and Standard Deviation.

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3.8.8 Profile and Ruler Tool
Measure and cut profiles on surface using the two icons shown below. This can be useful when measuring and diagnos-
ing artifacts and contacts. To adjust the label size, select Ctrl + or Ctrl- accordingly.

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3.9 Step 9: Exporting
There are many export options that can be useful for project applications, however just Tides, XYZ (processed line by line
and grided), and GeoTIFF (grid) are mentioned here. See the Qimera manual for more information. Most additional exports
will be made in Global Mapper in the office.
FULL DELIVERABLES SHOULD ONLY BE MADE IF/WHEN PROCESSING IS COMPLETE FOR AN AREA AND DATA ARE IN SPEC.
THIS WILL OFTEN ONLY BE DONE BY THE OFFICE.
The commonly required deliverables straight out of Qimera are line by line Tides, Line by Line Raw and Processed XYZ,
grided XYZ, TPU, Density and line by line backscatter GSF. Other grids and deliverables will be produced in the office once
the 50cm Grid are compiled so they can be tiled first. All files need to be brought in to Qimera even if they will not be
used in the Grid.
As with other sensors, exports should NOT live within the project. This causes the projects to often be 100+ GB larger
than they need to be and cause additional headaches when trying to copy to and from the server. Move all export to their
respective deliverable folders.
Vessel: 01_XX_2020-004\01_Data\03_Deliverables\01_Rev00_Data_Deliverables
Office: 01_XX_2020-004\01_Data\03_Deliverables\01_Rev01_Data_Deliverables
3.9.1 XYZ
Before adding final deliverables to the server, always verify that the surfaces were exported correctly by loading them
into Global Mapper.
3.9.1.1 Surface (gridded)
1. Export → Dynamic Surface → To Surface…
2. To quickly open the Project directory, hold Control and hit F.

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3. Select Export Floating Point GeoTIFF. Save in TIFF folder The default folder location will be the Export folder
in the working Qimera project – save in the GeoTIFF created folder.
4. If required, an XYZ can be exported following the same procedure and choosing XYZ.
5. It is common for shallow or minimum depth layer to be exported as well. The mean and shallow depth
surfaces are created by selecting Dynamic Surface → Snapshot as Static Surface. These will then show up
under “Project Layers” as “Static Surfaces.”
6. To export Static surfaces, with the surface selected, go to Export → Static Surface → Export to Surface

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3.9.1.2 Surface Statistics (gridded)
Other common exports for final deliverables include Density, Standard Deviation, THU, and TVU. Different
projects have different requirements which can be found in the PEP. These statistical surfaces need to be
exported, as well as entered into the Processing Log.
The logs generally require minimum, maximum, and average values of these surfaces. The values can be found
by viewing the histogram of these surfaces. Select the desired surface, go to the colormap drop down and select
“Adjust Colormap Range…”
For all statistical grids (except THU and TVU), select Dynamic Surface → Extract Dynamic Surface Layer.

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To create the THU and TVU layers, go to Dynamic Surface → Create THU and TVU layers. This step may take a
few minutes depending on the size of your zone.
The statistical surfaces, including THU and TVU will show up under “Project Layers” as “Sd Objects.”
To Export a Sd Object, go to Export → Scalar Object → Export to Surface

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3.9.1.3 Line by Line (Ungridded)
1) Highlight all *.db files to Export, and Navigate to Export Raw Sonar File Export to ASCII…
2) Be sure that Footprint X, Y, and Z are checked under Fields.
3) Under Format Options, be sure the Separator is set to Comma. DO NOT check Include Header.
4) Under Data Options, DO NOT check Invert Z. Click on Filter Soundings… The Filter Window will appear; Check
“Accepted Soundings Only” for Processed XYZ
5) Under Output Coordinate System, select the project designated system from either the drop-down menu or by
manually entering the ESPG code (NAD83 (2011) UTM18N, ESPG Code 6347).
6) Under Export Options, be sure the select “Convert each file individually” and then navigate to
01_XXBordelon_2020-
004\01_Data\03_Deliverables\01_Rev00_Data_Deliverables\02_Bathymetry_Data\01_Line_XYZ_Data\02_Proce
ssed.

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1
3
2 3
**NOTE: Under Data Options, be sure to set “Accepted Soundings Only” when exporting Processed XYZs. To export Raw
XYZs select “All soundings regardless of status” **
3.9.2 GSFs
Prior to backscatter processing in FMGT, *.GSF files will need to be exported from Qimera upon the completion of MBES
processing. Only after an area has been approved by the SME in the office as final can the GSFs be exported. Backscatter
processing is to be done from cleaned, processed MBES; any additional edits or changes to MBES data require a re-ex-
port of GSFs. Because of this, *.GSF exports are only created in the office.
Exporting a GSF will cause Qimera to read the QPD files that are created when the raw MBES *.DB files are imported.
These QPDs contain all changes made during Qimera processing to provide a processed MBES Backscatter file in the
form of *.GSF for use in FMGT. Once MBES processing is completed in Qimera, highlight all the Raw Sonar Files that re-
quire *.GSF exports and either navigate to Export > Raw Sonar File > to GSF or right click and in the dropdown select Ex-
port > to GSF.

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The following window will appear: GSF Export Options. This is where the specific systems and settings for the *.GSF files
are chosen. There should be Head 1 and Head 2 listed for the OWF Dual Head MBES system, so be sure both Heads are
checked on. Under GSF Options, select to Include water column picks and include raw backscatter imagery.
Selecting OK will begin the *.GSF export. This can take some time depending on the number of files within the project.
These files will automatically be saved to the Qimera project’s Export folder. These will need to be saved to the server:
01_XX_2020-004\01_Data\03_Deliverables\02_Rev01_Data_Deliverables\02_Bathymetry_Data\08_Pro-
cessed_GSF_Files

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4. PROCESSING A PATCH TEST
Below is a summary of how to process a patch test in Qimera. Provided below is a link to the QPS ‘How-to Time – Processing
a Patch Test’ for additional guidance and information.
https://confluence.qps.nl/qimera/latest/en/how-to-qimera-processing-a-patch-test-174096518.html
1. Ensure all offsets are correct in the vessel file and all angular/time offsets are removed. To do this, go to the
Vessel Editor in the Tools menu and set Pitch, Roll, and Heading values to 0. Tools Vessel Editor
**NOTE: For using a dual head, be sure to zero out both sensor’s pitch, roll, and heading values. For using a tilted
mount, leave the larger Roll bias (~30 deg) in the vessel file. **
2. Select the best fitting survey lines to calibrate for Latency, Heave, Pitch, Yaw, and Heading.
3. Go to the Patch Test Tool in the Tools menu. It may be helpful to generate a Dynamic Surface and/or Static
Surface first, to monitor pre- and post- calibrations. Tools → Patch Test Tool
4. Qimera will automatically select average placement of currently selected lines. However, this is not usually
the best location, and sometimes not even the best pair of lines to choose, so reselect the best lines and re-
draw the slice over a nice overlapping section. This applies for all patch test parameters.
**When using a dual-head system, be sure to process the patch corrections for Port and Starboard heads
separately**
** Note: In Qimera, Starboard Up = negative; Starboard Down = positive. **

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4.1 ROLL
Select two reciprocal lines that were surveyed in opposite directions (Heading of 0 and 180 for example) at roughly the
same speed over flat seafloor. Draw the slice across the swath (i.e., The small box drawn should look perpendicular to
the lines, as shown below).
1. Select Roll from the Offset dropdown and properly place the slice (make it thin). Hit the auto
solve button.
2. Once the solution is complete, manually fine tune the roll value until a best alignment is
obtained. For finer adjustments, hold ctrl while moving the slider. Once satisfied with the
offset value, save the results for Roll by clicking the ‘Add Calibration’ button. Then move on
to the next test, Pitch.

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4.2 PITCH
Select two reciprocal lines that were surveyed in opposite directions at the same speed over the target. Draw the slice
along the swath (i.e., The small box drawn should look parallel to the lines, as shown below).
1. Select Pitch from the Offset dropdown and properly place the slice (make it thin). Hit the
auto solve button.
2. Once the solution is complete, manually fine tune the pitch value until a best alignment is
obtained. Once satisfied with the offset value, save the results for Pitch by clicking the ‘Add
Calibration’ button. Then move on to the next test, Yaw/Heading.

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4.3 YAW/HEADING
Select two offset lines that were surveyed in the same direction at the same speed on either side of the target. Draw the
slice along the swath (i.e., The small box drawn should look parallel to the lines, as shown below). For this test, the tar-
get should be in the outer beams of the two lines selected where the swath overlaps.
1. Select Heading from the Offset dropdown and properly place the slice (make it thin). Hit the
auto solve button.
2. Once the solution is complete, manually fine tune the roll value until a best alignment is
obtained. Once satisfied with the offset value, save the results for Heading by clicking the
‘Add Calibration’ button.

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3. Once all tests have been confirmed, Save and Apply all values in the Patch Test window
Always confirm that the values have applied to the vessel file.

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5. TROUBLESHOOTING
QPS JIRA is the online help desk/ticket system. Serious data issues or bugs with the software should be addressed to QPS
directly through a help ticket, once discussed with the PM/SME. The website is listed here:
https://jira.qps.nl/secure/Dashboard.jspa
Additional guides and tools can also be found on their website for Qimera Documentation:
https://confluence.qps.nl/qimera/latest/en/qimera-documentation-151127947.html
5.1.1 Wobble Tool

The Wobble Analysis Tool is very helpful for determining motion and offset issues with a dataset. Once a dynamic sur-
face is made, and an artefact becomes apparent in the data. To troubleshoot:
1. Select the line and navigate to Tools → Wobble Analysis Tool…
2. Move/resize the selection box in the map view to get the best view of the data. If unfamiliar with the
different options, play around with the Multibeam and Motion Sensor options in the Wobble Test
Control (Shown above) to see what changes they make to the data. To reset any value, click the reset
button to the right.

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3. After confirming the results from the Wobble Analysis, save the results if any of the options fixed the artefact.
Then, highlight and reprocess the affected lines.

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2023-001

QIMERA MULTIBEAM PROCESSING

Ocean Winds NY Bight 0537

Bluepoint Wind Project

2. ABBREVIATIONS & DEFINITIONS

3. CODE, STANDARDS & REFERENCE MATERIAL

3rd Party References

4. ROLES & RESPONSIBILITIES

TERRASOND - CONFIDENTIAL AND PROPRIETARY

TERRASOND - CONFIDENTIAL AND PROPRIETARY

TERRASOND - CONFIDENTIAL AND PROPRIETARY

2023-001_QIMERA PROCESSING GUIDE Page 3

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3.1 Step 1: Project setup and update

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3.1.2 STEP 1B - Configure Shortcuts

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…from D:\07_Vessel_Config into the Qimera Project Folder D:\01_QIMERA_Projects\2020-004_Sarah_Bor-

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Be sure to QC both the Port and Starboard MBES Head Uncertainty.

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3.5.1 Importing SBET and RMS

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3.5.2 Importing Tide Files

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3.6.1 RTK (Accurate Height)

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3.7.1.2 Slice Editor, 2D

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Below are some examples of what noise / outliers should be cleaned:

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Before weak Spline After weak Spline

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Note: In Qimera, Starboard Up = negative; Starboard Down = positive.