usage: happy-ann2happy [-h] -i DIR [DIR ...] [--regexp REGEXP]
[-c {pixels,polygons,pixels_then_polygons,polygons_then_pixels}]
[-r] [-o DIR] -f {flat,dir-tree,dir-tree-with-data} -l
LABELS [-N] [-u UNLABELLED]
[--black_ref_locator LOCATOR]
[--black_ref_method METHOD]
[--white_ref_locator LOCATOR]
[--white_ref_method METHOD]
[--white_ref_annotations FILE]
[--black_ref_locator_for_white_ref LOCATOR]
[--black_ref_method_for_white_ref METHOD]
[--pattern_mask PATTERN] [--pattern_labels PATTERN]
[--pattern_png PATTERN] [--pattern_opex PATTERN]
[--pattern_envi PATTERN] [-I] [-n] [--resume_from DIR]
[-V {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
Turns annotations (PNG, OPEX JSON, ENVI pixel annotations) into Happy ENVI
format.
optional arguments:
-h, --help show this help message and exit
-i DIR [DIR ...], --input_dir DIR [DIR ...]
Path to the PNG/OPEX/ENVI files (default: None)
--regexp REGEXP The regexp for matching the ENVI base files (name
only), e.g., for selecting a subset. (default: None)
-c {pixels,polygons,pixels_then_polygons,polygons_then_pixels}, --conversion {pixels,polygons,pixels_then_polygons,polygons_then_pixels}
What annotations and in what order to apply
(subsequent overlays can overwrite annotations).
(default: pixels_then_polygons)
-r, --recursive whether to look for OPEX/ENVI files recursively
(default: False)
-o DIR, --output_dir DIR
The directory to store the fake RGB PNG images instead
of alongside the HSI images. (default: None)
-f {flat,dir-tree,dir-tree-with-data}, --output_format {flat,dir-tree,dir-tree-with-data}
Defines how to store the data in the output directory.
(default: dir-tree-with-data)
-l LABELS, --labels LABELS
The comma-separated list of object labels to export
('Background' is automatically added). (default: None)
-N, --no_implicit_background
whether to require explicit annotations for the
background rather than assuming all un-annotated
pixels are background (default: False)
-u UNLABELLED, --unlabelled UNLABELLED
The value to use for pixels that do not have an
explicit annotation (label values start after this
value) (default: 0)
--black_ref_locator LOCATOR
the reference locator scheme to use for locating black
references, eg rl-manual; requires: dir-tree-with-data
(default: None)
--black_ref_method METHOD
the black reference method to use for applying black
references, eg br-same-size; requires: dir-tree-with-
data (default: None)
--white_ref_locator LOCATOR
the reference locator scheme to use for locating
whites references, eg rl-manual; requires: dir-tree-
with-data (default: None)
--white_ref_method METHOD
the white reference method to use for applying white
references, eg wr-same-size; requires: dir-tree-with-
data (default: None)
--white_ref_annotations FILE
the OPEX JSON file with the annotated white reference
if it cannot be determined automatically (default:
None)
--black_ref_locator_for_white_ref LOCATOR
the reference locator scheme to use for locating black
references that get applied to the white reference, eg
rl-manual (default: None)
--black_ref_method_for_white_ref METHOD
the black reference method to use for applying black
references to the white reference, eg br-same-size
(default: None)
--pattern_mask PATTERN
the pattern to use for saving the mask ENVI file,
available placeholders: {SAMPLEID} (default: mask.hdr)
--pattern_labels PATTERN
the pattern to use for saving the label map for the
mask ENVI file, available placeholders: {SAMPLEID}
(default: mask.json)
--pattern_png PATTERN
the pattern to use for saving the mask PNG file,
available placeholders: {SAMPLEID} (default:
{SAMPLEID}.png)
--pattern_opex PATTERN
the pattern to use for saving the OPEX JSON annotation
file, available placeholders: {SAMPLEID} (default:
{SAMPLEID}.json)
--pattern_envi PATTERN
the pattern to use for saving the ENVI mask annotation
file, available placeholders: {SAMPLEID} (default:
MASK_{SAMPLEID}.hdr)
-I, --include_input whether to copy the PNG/JSON file across to the output
dir (default: False)
-n, --dry_run whether to omit generating any data or creating
directories (default: False)
--resume_from DIR The directory to restart the processing with (all
determined dirs preceding this one get skipped)
(default: None)
-V {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --logging_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
The logging level to use. (default: WARN)