Menu Process > Processing Options... > 3. DSM, Orthomosaic and Index > Index Calculator - PIX4Dmapper


This article describes the feature options in each section of the Index Calculator tab in the Processing Options window.

Index > Interface > Menu Process  Previous  |  Next 
Access: On the Menu bar, click Process > Processing Options..., the Processing Options pop-up appears. Click 3. DSM, Orthomosaic and Index.


1. Initial Processing

2. Point Cloud and Mesh

3. DSM, Orthomosaic and Index

Resources and Notifications


DSM and Orthomosaic Additional Outputs Index Calculator  

Allows the user to change the processing options and outputs related to the Index Calculator. These are processed during step 3. DSM, Orthomosaic and Index.

These settings come in 4 sections:

  • Radiometric Processing and Calibration: Allows the users to calibrate and correct the image reflectance, considering the illumination and sensor influence. 
  • Resolution: Allows the user to set the resolution as well as the downsampling method (if needed).
  • Reflectance Map: Allows the user to decide if the Reflectance Map(s) will be generated while processing step 3. DSM, Orthomosaic and Index, and if the Tiles will be merged.
  • Indices: Shows the list of indices either from the database or created by the user. Allows the user to select which indices are generated while processing step 3. DSM, Orthomosaic and Index. For the selected indices, the Index Map is saved as a GeoTIFF, the Index Map Grid as a .shp file, the Classes as a .shp file, and the Classes with color representation as a .jpg file.
  • Export: Allows the user to select some desired outputs.


Step 3 Index Calculator.jpg


Radiometric Processing and Calibration

Allows the users to calibrate and correct the image reflectance, considering the illumination and sensor influence. It is possible to choose the type of radiometric correction to be done:

  • No correction: no radiometric correction will be done
  • Camera only: corrections will be applied to the parameters that are written in the EXIF metadata and relate to the camera (vignetting, dark current, ISO, etc...): Exif/Xmp tags required for radiometric correction for multispectral camera
  • Camera and Sun Irradiance: corrections will be applied to the camera parameters (same as using the option Camera only) as well as for the sun irradiance information written in the XMP.Camera.Irradiance EXIF tag.
  • Camera, Sun Irradiance and Sun angle: corrections will be applied to the camera parameters and the sun irradiance information (same as using the option Camera and Sun Irradiance) as well as to take into account the sun position. This option should only be chosen for flights that were done in clear-sky conditions. 
  • Camera, Sun Irradiance and Sun angle using DLS IMU: Same as the previous one but does not need to have a fixed position and angle between the camera and DLS sensor. The orientation is tagged from the IMU embedded in the sun sensor.

The camera used is displayed. Users can calibrate the sensor to perform an illumination adjustment in order to obtain more accurate reflectance values. If there are more than one camera model in the project, all the cameras will be listed in the Radiometric Processing and Calibration section.

The Calibrate button allows us to consider the information from a picture with a radiometric calibration target if such a target was used during the project. After clicking Calibrate for a camera model, the Radiometric Calibration pop-up appears:

Radiometric Calibration window in PIX4Dmapper

The Radiometric Calibration pop-up has 2 sections:

  • Image: The image section allows the user to browse the image that will be used for the radiometric calibration.
  • Reflectance Factor: The Reflectance Factor section allows the user to set the reflectance values for the calibration target. 


In File Name, the Browse button, opens the Select a radiometric calibration image pop-up. This pop-up allows the user to select the image in which the radiometric calibration target appears.

When an image is browsed, the user can draw a region on the image that will define the radiometric calibration. The Reset button, resets the area drawn by the user. 

Calibration target radiometric calibration window in PIX4Dmapper

Reflectance Factor

In the Reflectance Factor section, the detected bands of the camera model appear. This section allows the user to type the reflectance values for the calibration target for the bands of the camera model selected.

Important: The reflectance values can be between 0.0 and 1.0.

For more information about the radiometric calibration target: Radiometric calibration target - PIX4Dmapper.

Reflectance factor in PIX4Dmapper's index calculator

and the action buttons:

    • OK: Confirms the radiometric calibration.
    • Cancel: Does not save the radiometric calibration.
    • Help: Opens the PIX4Dmapper help.


Allows the user to set the resolution for the reflectance map. If a resolution lower than 1 GSD is chosen, the downsampling method can be chosen among the following options. Note that the window size will depend on the downsampling rate:

  • Gaussian Average: Apply a Gaussian filter to the image.
  • Fast Gaussian: This option performs the downsampling on the original images (hence does not produce a 1GSD reflectance map first), resulting in faster processing time.
  • Average: The pixel takes the average value of the window around it.
  • Median: The pixel takes the median value of the window around it.
  • 75% Quantile: The pixel takes the value of the 75% quantile of the window around it. 
  • Minimum pixel: The pixel takes the minimal pixel value of the window around it. 
  • Maximum pixel: The pixel takes the maximal pixel value of the window around it. 

Reflectance Map

Allows users to generate and save the Reflectance Map in GeoTIFF format.

  • GeoTIFF: The Reflectance Map is generated and saved in GeoTIFF format during the step 3. DSM, Orthomosaic and Index
    • Merge Tiles: For most projects, the Reflectance Map is split into tiles where every tile is in GeoTIFF format. This option generates a single Reflectance Map file by merging all the individual tiles.

      When this box is deselected, the merged Reflectance Map file is not generated, and users will only find smaller tiles in the result folder.


Allows the user to select which indices are generated while processing step 3. DSM, Orthomosaic and Index (If in the section Reflectance Map, Geotiff is selected), and generates the Index Map Grid and the Classes for the selected indices. The resolution of the Index Map generated is the same as the Reflectance Map.

  • Indices Box: All indices are displayed in the gray box with icons:


Allows the user to select some desired outputs:

  • Index Values as Point Shapefiles (.shp): This map is generated while generating the Index Map. The Index Map Grid is generated by placing a grid in the Index Map. If a grid point lays on exactly 1 pixel, it takes the value of the pixel of the Index Map. If a point lays on several pixels, its value is interpolated with the values of the neighboring cells of the Index Map.
    • Grid Size [unit/grid]: Defines the grid size. The default value is 200 cm/grid. 
      Note: The maximum value that can be entered is 10000.



  • Index Values and Rates as Polygon Shapefiles (.shp): Allows the user to export the index values and rate regions as a .shp file. 
    • Grid Size [unit/grid]: Defines the grid size. The default value is 400 cm/grid.
      Note: The maximal value that can be entered is 10000.




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Article feedback (for troubleshooting, post here instead)


  • Dor Har

    You haven't tell much about the reflectance factor-

    Can I get the reflectance factor from the automatic factor that the software gives me?

    Should I look for this factor in the calibration panel? Because I've got here 5 (and not six - for the Altum) numbers between 51 to 53, near each band's lens.

    So, what's about the sixth band (Thermal camera)? I can calibrate him as well...

    Waiting for your reply,


  • Fernanda Bosmediano

    Hi Dor

    You can find the reflectance values printed on the panel. The values normally are given in percentage, so you need to write the values as decimal fractions when using Pix4Dmapper. If you do not see the reflectance values on the panel, please contact the camera manufacturer.  Please be aware that the thermal band (LWIR) does not require the calibration coefficient, therefore you can leave the corresponding field for it empty in the Panel Calibration section.




    Edited by Fernanda Bosmediano
  • Cassidy Rankine

    The DN values from my spectral reflectance maps (using Micasense Altum camera) are really high in the exported tiles for some reason.
    Values are in the 10,000's for any given spectral band map in the tiles, but are normal (expected) values scaled from 0 to 1 in the merged ortho


    Any idea why the tiled DNs are so high and uncorrelated with the proper reflectance values in the full ortho?

  • Avatar
    Momtanu (Pix4D)

    Hi Cassidy,

    The radiometric target must be used for radiometric calibration to get the reflectance values normalized between 0-1. The reflectance tiles also should give the same values as the reflectance map.

    Orthomosaics should not be used for the multispectral images as they are not radiometrically calibrated and we color balance them. Can you confirm that you are talking about the reflectance map and the reflectance tiles?

  • Juho-Ville Marttila

    Hey, I tried to test radiometric calibration with Pix4Dmapper trial version 4.5.6, but I got the text "Radiometric Processing and Calibration (Not avaible in this edition)". The menu is gray and not in use. Is this caused by trial stage, or version, or something else?

  • Avatar
    Momtanu (Pix4D)

    I think you are using the discovery version which is a free version and has step 3 disabled. You will need to log out and log in again. When you log in, select Pix4DMapper as the license.

  • Juho-Ville Marttila

    Thanks for your reply. You are right: I only has the discovery version, even if I followed the links for getting Pix4Dmapper trial. How I assign Pix4Dmapper trial to my account? I got Pix4Dcloud trial. Does it effect if I can use Pix4Dmapper trial?

  • Avatar
    Momtanu (Pix4D)

    You will need to reach out to sales to get a Pix4DMapper trial. First, you can try getting it from here:

    You can try any number of software you want at one time, having a Pix4D cloud trial will not come in the way of getting a Pix4DMapper trial.

    Edited by Momtanu (Pix4D)
  • Eddison Araya

    Hola un gusto saludar!! tengo una duda con la camara Micasense Altum, la cual usa el sensor de Luz LSD.

    Si se usa la opcion Cámara e irradiancia solar , en ella se utiliza el sensor de luz incidente LSD?

    Me queda claro que con la opción Camara, solo son los datos del panel.





  • Fernanda Bosmediano

    Hola Edison, 


    Si se utiliza la información del sensor de luz. Puedes ver más información en este link:


    Edited by Fernanda Bosmediano
  • Eddison Araya

    Gracias! acabo de ingresar a ese link y dejar una pregunta.

    Un saludo



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