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back Reports schema

A description of the file formats of the different available reports.

Project and volume reports

Most report types can be requested for a whole project as well as for individual volumes. A project report is a convenience feature which requests reports for all individual volumes of the project at once and provides a ZIP file containing the volume reports for download. However, not all configuration options may be available for project reports.

The following sections describe the different types of volume reports but, per definition, apply for project reports as well.

Annotation reports

Basic

The basic annotation report contains a graphical plot of abundances of the different annotation labels (annotations can have multiple labels by different users). If the annotations should be separated by label tree, there will be one plot for each label tree that was used.

Example plot:

The bars of the plot are color-coded based on the colors of the labels they represent. If any label occurs more than a hundred times, a logarithmic scale is applied.

Extended

The extended annotation report is an XLSX spreadsheet which contains a list of the abundances of each label and image. If the annotations should be separated by label tree, there will be one worksheet for each label tree that was used.

For a single worksheet (not separated by label tree) the first line contains the volume name. For multiple worksheets the first lines contain the name of the respective label tree. The second line always contains the column headers. The columns are as follows:

  1. Image filename
  2. Label hierarchy

    The label hierarchy contains all label names from the root label to the child label, separated by a >. If we have the following label tree:

    Animalia
    └─ Annelida
       └─ Polychaeta
          └─ Buskiella sp
    
    Then the content of the "label hierarchy" column for annotations with the label "Buskiella sp" will be Animalia > Annelida > Polychaeta > Buskiella sp.

  3. Label abundance

Area

The annotation area report is an XLSX spreadsheet of all area annotations (rectangle, circle, ellipse and polygon) with their width and height in pixels (px) and their area in px². If a laser point detection was performed, the width and height in m and the area in m² is included as well.

The computed area of self-intersecting polygons like these will not be correct!

For a single worksheet (not separated by label tree) the first line contains the volume name. For multiple worksheets the first lines contain the name of the respective label tree. The second line always contains the column headers. The columns are as follows:

  1. Annotation ID
  2. Annotation shape ID
  3. Annotation shape name
  4. Label IDs comma separated list of IDs of all labels that are attached to the annotation
  5. Label names comma separated list of names of all labels that are attached to the annotation
  6. Image ID
  7. Image filename
  8. Annotation width (m) Rectangle: the longer edge. Circle: the diameter. Ellipse: Length of the major axis. Polygon: width of the minimum (non-rotated) bounding rectangle.
  9. Annotation height (m) Rectangle: the shorter edge. Circle: the diameter. Ellipse: Length of the minor axis. Polygon: height of the minimum (non-rotated) bounding rectangle.
  10. Annotation area (m²)
  11. Annotation width (px) See the width in m for the interpretation of this value for different shapes.
  12. Annotation height (px) See the height in m for the interpretation of this value for different shapes.
  13. Annotation area (px²)

Full

The full annotation report is an XLSX spreadsheet similar to the extended report. It contains a list of all annotations and their labels.

The columns are as follows:

  1. Image filename
  2. Annotation ID
  3. Annotation shape name
  4. X-Coordinate(s) of the annotation (may span multiple lines)
  5. Y-Coordinate(s) of the annotation (may span multiple lines)
  6. Comma separated list of label hierarchies (see the extended report on how to interpret a label hierarchy)
  7. The area of the image in m² if available

For the different annotation shapes, the coordinates are interpreted as follows:

  • Point: The x and y coordinates are the location of the point on the image.
  • Rectangle: Each line contains the x and y coordinates of one of the four vertices describing the rectangle.
  • Circle: The first line contains the x and y coordinates of the center of the circle. The x value of the second line is the radius of the circle.
  • Ellipse: Similar to the rectangle. The first two vertices are the end points of the major axis. The next two vertices are the end points of the minor axis.
  • Line string: Each line contains the x and y coordinates of one of the vertices describing the line string.
  • Polygon: Each line contains the x and y coordinates of one of the vertices describing the polygon.

CSV

The CSV report is intended for subsequent processing. If you want the data in a machine readable format, choose this report. The report is a ZIP archive, containing a CSV file. The CSV file name consists of the volume ID and the volume name (cleaned up so it can be a file name) separated by an underscore. If the annotations should be separated by label tree, there will be one CSV file for each label tree and the CSV file name will consist of the label tree ID and name instead.

Each CSV file contains one row for each annotation label. Since an annotation can have multiple labels, there may be multiple rows for a single annotation. The first row always contains the column headers. The columns are as follows:

  1. Annotation label ID (not the annotation ID)
  2. Label ID
  3. Label name
  4. Label hierarchy (see the extended report on how to interpret a label hierarchy)
  5. ID of the user who created/attached the annotation label
  6. User firstname
  7. User lastname
  8. Image ID
  9. Image filename
  10. Image longitude
  11. Image latitude
  12. Annotation shape ID
  13. Annotation shape name
  14. Annotation points

    The annotation points are encoded as a JSON array of alternating x and y values (e.g. [x1,y1,x2,y2,...]). For circles, the third value of the points array is the radius of the circle.

  15. Additional attributes of the image

    The additional attributes of the image are encoded as a JSON object. The content may vary depending on the BIIGLE modules that are installed and the operations performed on the image (e.g. a laser point detection to calculate the area of an image).

Image label reports

Basic

The basic image label report is an XLSX spreadsheet similar to the extended annotation report. It contains a list of all labels attached to each image of the volume. The columns are as follows:

  1. Image ID
  2. Image filename
  3. Comma separated list of label hierarchies (see the extended annotation report on how to interpret a label hierarchy)

CSV

The CSV report is similar to the annotation CSV report. If you want the data in a machine readable format, choose this report.

Each CSV file contains one row for each image label. Since an image can have multiple different labels, there may be multiple rows for a single image. The columns are as follows:

  1. Image label ID
  2. Image ID
  3. Image filename
  4. Image longitude
  5. Image latitude
  6. ID of the user who attached the image label
  7. User firstname
  8. User lastname
  9. Label ID
  10. Label name
  11. Label hierarchy (see the extended annotation report on how to interpret a label hierarchy)