Small utilities to aid working with the SOF dataset
Project description
SOF-Utils
Utility scripts to aid working with the SOF dataset.
Command Line Tools
sof-dicom-meta
usage: sof-dicom-meta [-h] [-r] [-f FILE] [-p] [-s] dicom_path
Extract dicom meta info in csv format.
positional arguments:
dicom_path Path to search for dicom files in.
optional arguments:
-h, --help show this help message and exit
-r Inlcude subdirectories
-f FILE, --file FILE Write output to file instead of stdout.
-p, --progress Shows a progressbar, only available in combination
with -f.
-s, --statistics Print minimum and maximum values for each column.
sof-dicom-corrupted
usage: sof-dicom-corrupted [-h] [-r] [-f FILE] [-p] [-d] [-s] dicom_path
Find corrupted dicom files.
positional arguments:
dicom_path Path to search for dicom files in.
optional arguments:
-h, --help show this help message and exit
-r Inlcude subdirectories
-f FILE, --file FILE Write output to file instead of stdout.
-p, --progress Shows a progressbar, only available in combination
with -f.
-s, --summary Print summary.
sof-export-images
usage: sof-export-images [-h] [-V] [--data_dir DATA_DIR]
[--configuration CONFIGURATION] [--format {png,jpeg}]
[--width WIDTH] [--height HEIGHT] [--split_lr]
[--flip_lr] [--visits VISITS] [--include INCLUDE]
[--exclude EXCLUDE] [--max-group-size MAX_GROUP_SIZE]
[--num-groups NUM_GROUPS] [--randomized-groups]
[--zip]
target_path
Exports the SOF_hip dataset as png images
positional arguments:
target_path Path to place the images in.
optional arguments:
-h, --help show this help message and exit
-V, --version Print the version string
--data_dir DATA_DIR, -d DATA_DIR
Path to the TFDS dataset.
--configuration CONFIGURATION, -c CONFIGURATION
Dataset configuration.
--format {png,jpeg}, -t {png,jpeg}
Output image format, default to png
--width WIDTH, -w WIDTH
Target width of the exported images
--height HEIGHT, -g HEIGHT
Target height of the exported images
--split_lr, -s Split radiographs vertically into a left and a right
half. The exported files will get a "L" or "R"
postfix, depending on the side of the hip that is
shown. Note that the left hip is usually shown on the
right hand side of the radiograph. If the (possibly
downscaled) image does not have an even width, it is
padded with one additional volumn to the right.
--flip_lr, -p Flips the images of the left hip so that they look
like a right hip. Can only be used in combination with
--flip_lr
--visits VISITS, -v VISITS
Comma separated list of visits to export. If this
option is omitted, all visits are exported.
--include INCLUDE Only include the IDs listed in given file. The IDs
should be listed one ID per line.
--exclude EXCLUDE Exclude the IDs listed in given file. The IDs should
be listed one ID per line.
--max-group-size MAX_GROUP_SIZE
Splits the exported images into groups. The groups
will contain at most the specific number of files.
Cannot be used together width --num-groups
--num-groups NUM_GROUPS
Splits the exported images into the specified number
of groups. Cannot be used together with --max-group-
size.
--randomized-groups If grouping is used (either with --max-group-size or
with --num-groups), the assignment of files to groups
will be randomized.
--zip, -z Write exported images to a zip file instead of into a
directory. If grouping is enabled, one zip file per
group will be created. Without grouping 'target_path'
should be a path a the target zip file not to an
directoty.
sof-convert-labels
usage: sof-convert-labels [-h] [-V] [-f FILE] [-s SKIP_FILE] input_label_file
Convert proximal femur labels from LabelStudio JSON_MIN format to csv format
positional arguments:
input_label_file Path to input label json file(s). Multiple files can
be used using glob pattern.
optional arguments:
-h, --help show this help message and exit
-V, --version Print the version string
-f FILE, --file FILE Write output to file instead to stdout
-s SKIP_FILE, --skip-file SKIP_FILE
Write skipped file names to the given file.
sof-convert-tfds
usage: sof-convert-tfds [-h] [--data_dir DATA_DIR] [-V]
[--configuration {keypoint_detection}]
[--format {TFObjectDetection}] [--split SPLIT]
[--num_shards NUM_SHARDS]
output_file
Convert SOF_hip TFDS dataset into another format.
positional arguments:
output_file Path to destination file.
optional arguments:
-h, --help show this help message and exit
--data_dir DATA_DIR TFDS data dir.
-V, --version Print the version string
--configuration {keypoint_detection}, -c {keypoint_detection}
Dataset configuration to use. Note: not all
configuration are supported by all output format.
Default is 'keypoint_detection'
--format {TFObjectDetection}, -f {TFObjectDetection}
Dataset configuration to use. Note: not all
configuration are supported by all output format.
Default is 'TFObjectDetection'
--split SPLIT, -s SPLIT
Split to convert. Default to 'train'
--num_shards NUM_SHARDS, -n NUM_SHARDS
Number of shards to split the resulting dataset into.
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