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Qimera - Processing

This page contains frequently asked questions for Qimera.

On this page:

I have a skull and crossbones next to my raw files, what does this mean?

This means that the data you brought into Qimera doesn't contain enough information to process it.  Here are two examples:

1) Reson .s7k file may only contain ping information (ranges and angles for the multibeam measurements) without containing information for position, motion, SVP, etc, in the source file. Qimera cannot process this data without the additional information.  If you import external navigation, motion, etc, then the skull and crossbones will disappear. 

2) In case of relative positioning like USBL or object linking in data collected in Qinsy, Qimera needs the QPD object track for the navigation. If you experience a  skull and crossbones when Qinsy db files are loaded, you will need to replay the files in Qinsy and have Qinsy to create the QPD files before reading the project in Qimera. 

Can I re-process data after cleaning?

The ideal workflow is to have the data processed before the validation/cleaning is done. You may encounter a situation in where your data was all validated and you find you need to re-process. This can be done under certain circumstances, the QPD sounding status will be retained, however, this will not work after a z-shift and re-process will re-set the z-shift. SBET application is an example of a z-shift. There may be a solution for your job and this needs to be looked at by a QPS Support engineer, so please do not hesitate to get in contact. 

How do I change the geodetic system of the project?

There may be a way to change the geodetics after the project was created and the data has been processed, without having to make a new project.  For example, if the project is created and you realize the geodetic setup was wrong.

A possible solution is depending on the scenario:

  • If the project input datum is correct and the output system is set up wrong, you may be okay by exporting to the different output system, for the client deliverable. It will be in the processed points export dialog.
  • If  at least one of the geodetic systems in the erratic project is correct (and the other is wrong), you may be okay re-projecting the project. This  needs to be done in the following way: set up a new Qimera project in the correct geodetic system (perhaps even a datum transformation), import the processed and validated data from the erratic project, telling Qimera what the system of the import data is and have Qimera perform the datum transformation at the import. 
  • If none of the above applies and you have encountered a different scenario, please contact QPS Support.

How is the Suggest Cell Size Calculated when building a surface?

When data is imported or reprocessed, we generate a histogram of the depths in the file.  When a user wants to grid a set of data, we normalize the histograms for each file and combine them into a master histogram for which we determine the depth associated with the highest count of soundings.  We calculate a footprint size at that water depth based on a 1 degree beamwidth assumption and then round this up to the nearest "nice" pixel size. For instance, instead of returning 0.42 m as the pixel size, it would return 0.50 m.  This is not meant to be an optimal or perfect cell size, but rather to help the user who may not fully know about cell size selection. The beamwidth assumption feature allows the user to create a map that is reasonable on their first try.  If the area covered by the selected lines has a wide range of depths, then the pixel size will not work well in both the deepest and the shallowest areas (you may get gaps or empty cells in the deep areas and low resolution in the shallow areas).  Also, the suggested cell size does not consider the sounding density at all.

What is the difference between Erase Invalid and Select Invalid when using the Swath Editor?

They are two different tools that allow for manual marking of soundings as invalid.  The "Erase" tool is a circle whose radius is controlled by the middle mouse wheel.  Left-click and hold down the mouse button and drag the cursor to "Erase" bad soundings.  This is inspired by Paint and Photoshop type cursor modes.  The "Select Invalid" mode allows a user to draw a rectangle box around soundings they want to remove.  Left-click and hold down the mouse button to draw a rectangle.  Soundings in the rectangle will be flagged as bad.  Edits in both modes can be undone with the "Undo" icon.

In the Processing Settings Editor what is, ‘Include time series data from adjacent lines closer than *.** seconds'? Should this ever be turned off or changed, and if so what is the optimum time scale?

It can happen on occasion that the first few pings in a data file will occur prior to the arrival of a navigation fix. For example in shallow water where the navigation comes in at 1 Hz and the mutlibeam might be pinging at 25 Hz. This can also happen at the end of a file. If we do nothing about this, you may find that gaps in coverage will occur at file breaks that occur along a survey line.

This setting allows the navigation and other time-series data lookup to sneak a peek at time-series from data files that occur immediately before and after the file being processed to give additional data points to interpolate over the gap.

Data files that are neighboring in time must be within 1 sec of the requested time in order to be considered. If the user is still seeing gaps, increasing the value to a slightly higher value may address the gap. There is not a good reason to ever disable this.


In the Processing Settings Editor how is the priority sorted out and assigned in the Position, Motion, Heading Tab? Do these come from the online settings or have their own criteria?

e.g. if an SBET file is added to the project does this have to be set as the primary motion source?

The priority source that was configured in real-time during acquisition is chosen if it is possible to deduce this from the source data file (e.g. .all and .db, but not .hsx and .s7k). If you add SBET or external navigation/motion, they are currently "promoted" to be the top priority source. The user can change the lookup priority in the Processing Configuration dialog box by bumping the desired data source item up to the top of the list.

What projections does QPS recommend for users who would prefer to work in unprojected space but are not able to?

Examples are users crossing multiple zones who do not want to create custom projections, and users in the research/scientific community who prefer working in unprojected space and prefer unprojected products.

Users will need to assess what projection is most suitable for their situation. There are three extra projections that were added to the common coordinate systems to support this re-projection issue - Mercator and Polar Stereographic projections for Arctic and Antarctic but there are no plans in the immediate future for others. 

Does Qimera automatically recognize the source file projection for any Raw Sonar data type?

The source file coordinate system and the project coordinate system are automatically recognized when importing QINSy DB files. For all other file types the coordinate information needs to be set manually. For the Kongsberg *.all and the RESON .s7k formats, it will assume the navigation data is in WGS84 lat/long. For Hypack HSX files these are always in a projected coordinate system which must be set manually. 

Does Qimera automatically recognize the source file projection for any Processed Points data type?

The source file coordinate system and the project coordinate system are automatically recognized when importing QINSy QPD files. For any other file type of Processed Point data, users must specify the projection. Qimera looks at the file to make an educated guess if it's projected or geographic. If it's geographic it will default to WGS84. If it's projected, and the Project's Coordinate System is set (which always has to be projected if it's set) it will default to the Project's coordinate system. If not, it will default to UTM North Zone 1. But remember, these are just default values, users still have to confirm or change them.

Does the option to export .GSF files from the source file menu export all soundings to .GSF regardless of status?

All soundings are exported. If they have been rejected for some reason, either through Blocking, Spline filtering, CUBE filtering, or manual editing, then the corresponding beam is marked as "Rejected" in the GSF. GSF flag capabilities are much simpler than what is supported with QPDs, so we can only mark a sounding as either good or bad in the GSF.

How does Export Processed Points from the source menu differ from Export Soundings in the Dynamic Surface menu?

Export Processed Points differs from Export Soundings in the Dynamic Surface because there are more formats to choose from (instead of just XYZ). Export Processed Points allows you to specify a different Z-value if exporting ASCII, and it can re-project to a different coordinate system. Probably the biggest difference is that you are dealing with individual files. This means you can pick a single file, or multiple files to export. You can also convert them to individual files, or merge the output into one big file. With the Dynamic Surface Export Soundings, you are exporting from all lines of data included with that Surface.

Is TPU re-calculated after SBET application?

The TPU is currently only recalculated if you 're-raytrace' the data. So, if you import SBET data for position or height, Qimera will 're-navigate' your data which is much faster than re-raytracing, however you will not get an updated TPU.

To update TPU:

  1. Import SBET, say 'no' when Qimera prompts you to re-navigate data.
  2. Update TPU parameters for the SBET system in the vessel configuration file. You will want to change the values to reflect what it actually is. Once you save the new vessel configuration, all the multibeam data files that are associated with the vessel file will be marked as requiring full re-raytrace. (If you have the SMRMSG file and the SBET file with the same names in the same folder, the SBET will take the TPU values from the SMRMSG file)
  3. Click the auto-process button to re-raytrace the data.

While cleaning data, if you open an area but didn’t change any soundings, how does one know which areas have already been worked on?

Currently this can only be tracked while editing data in the Slice Editor. Areas that have been viewed have a light grey overlay in the Surface Edit Overview dock. Areas that have been edited are overlayed with a light red colour. These overlays can be turned on or off by toggling the 'Show Visited / Edited' checkbox in the Surface Edit Overview menu. They can also be cleared by selecting 'Clear Visited/Edited' in the same menu. This overlay is unique to each dynamic surface.

Previously, Suspect Flagging was a way of testing CUBE before rejecting everything. What is the workaround for that now? 

We have suspect, plotted and feature flagging, but each user decides how to use them (PFM). 

It affects the soundings of the QPD - the dynamic surface gets updated for all layers.

  • It has to be based on the CUBE surface.
  • Create survey area

Will the Spline filter work on the Dynamic Surface or on the files?

The filter works on the QPD files but the results are updated in the Dynamic Surface. The Spline filter can either be applied to all the files that make up the Dynamic Surface, or by selecting files manually and running it on those files.

When you have a large survey and want to apply a Spline filter is is possible to constrain the filter to a smaller area or to only apply it to specific files? 

It is possible to apply the Spline filter to the full dynamic surface, specific files, and within a selected area.

When working on a Dynamic Surface, does it matter which layer you have selected? If you have the average layer selected are you then editing the average layer?

It doesn't matter which layer you have selected because when working on the Dynamic Surface, you are editing the soundings, not the layers (GRID file). The Dynamic Surface is broken down from the GRID file and the QPD’s. The QPD’s will keep the changes, and the GRID will get updated; editing is based on the points and the grid gets updated on it. The display is what you have selected: you should edit and see in the shallow surface; if you have CUBE you will be editing the CUBE surface.

Where does Qimera display/show the Source datum extracted from the Raw Data?

If you select a raw file and then go to the properties tab you will see the Coordinate System.
Whatever is shown in the properties tab for the raw file is what is being used as the basis for the transformation and projection to the project coordinate system.

There are some soundings from the noise at the sonar head and I don't want to see them. Can Qimera filter these soundings directly when I input the data?

You can use the processing settings to change the filters. For this kind of noise, you could filter either by either depth or range from the sonar.

In Qloud the ISO-44 standard (95% Posteriori Confidence Interval) is used for the Spline filter, is this the same in Qimera?


When I apply Patch Test results, the angular offsets are not the same for Tx and Rx transducers in the Vessel Editor, why?

Qimera separates the two transducers in its vessel offsets. The Patch Test Tool will apply the offset corrections to the transducer at which they will have an effect. Roll to Rx, Pitch and Heading to Tx. The values from the Patch Test can also be applied to the motion sensor data instead of the mounting offsets of the transducers.