ithron / sof-utils Goto Github PK

Is your feature request related to a problem? Please describe.
For nearly all supervised task, only the radiographs from the first visit should be used. Therefore, it would be more convenient to add a visit selection option to the sot-export-images tool than to manually delete unwanted visits after exporting.

Describe the solution you'd like
An option to select the visits to be exported should be added to sof-export-images.
The option should accept a list of visits (integer) that should be exported.
If not visit is given, all visits should be exported.

Describe alternatives you've considered
Export all visits and manually delete the unwanted visits afterwards.
However, this approach is suboptimal, since it requires exporting more images than required, resulting in longer run-times and disk space usage.

Is your feature request related to a problem? Please describe.
When exporting images using sof-export-images eg. for annotation training data, only IDs in the training set should be included, or the other way around, the IDs from the test set should be excluded.

Describe the solution you'd like
Add an option to sof-export-images to include or exclude IDs listed in a file.

Describe alternatives you've considered
Manual deletion of unwanted files after the export, but costs more time and disk space.

Describe the bug
There is at least one upside down radiograph in the dataset where sof-detect-keypoints labels both sides a 'Complete', one side with a high score and one side with a very low score and incorrect key point positions.
In this case the tool does not detect that the radiograph is upside down.

To Reproduce
Detect key points on SOF ID 41886 visit 1.

Is your feature request related to a problem? Please describe.
When images are exported using sof-export-images for annotation, the exported images must be grouped manually in order to distribute them to multiple annotators.
Manual randomized grouping, e.g. to split centers across annotators, is very difficult.

Describe the solution you'd like
There should be an option to sof-export-images to automatically, and optionally randomly, group the annotated images, e.g. by adding a group prefix to the file names or by exporting to different directories.

Describe alternatives you've considered

• Building a post-export script
  • would be a very specific tool and adds a lot of programming overhead
• Doing manual grouping
  • Tedious
  • Random grouping is not possible

Is your feature request related to a problem? Please describe.
Exporting images using sof-export-images is fine. But in order to use them in tools like LabelStudio, they must be contained in a ZIP archive. For a single group this can be easily done manually, but for grouped export an automated method would be preferable.

Describe the solution you'd like
Add option to sof-export-images to write the files directly to a ZIP archive, or to multiple archives is the grouping case.

Describe alternatives you've considered
Manual zipping is not an alternative.

The hip images can be split trivially into images of the left and right hip.

• If the (probabliy downsampled) image does not an even width, it should be padded to the nexy higher even width.
• The file names of the output files should be marked with 'L' or 'R' depedning wich part of the hip is show. Note: the right hip is usually shown in the left half of the radiograph.
• There should be an option to flip the result image L/R so that all images have the same orientation

Is your feature request related to a problem? Please describe.
The TFDS is easy to use, by the TF ObjectDetection API requires a simple .tfrecord file with a slightly different structure.

Describe the solution you'd like
Add a conversion tool to the package to convert between the SOF_hip TFDS dataset and the format required by TF ObjectDetection API.