usage: __main__.py [-h] [--data_type DATA_TYPE] [--exclude_background]
[-v [{DEBUG,INFO,WARNING}]] [-f]
{lower_threshold,upper_threshold,lower_threshold_eq,upper_threshold_eq,lower_threshold_otsu,upper_threshold_otsu,lower_clip,upper_clip,absolute_value,round,ceil,floor,normalize_sum,normalize_max,log_10,log_e,convert,invert,addition,subtraction,multiplication,division,mean,std,correlation,union,intersection,difference,concatenate,dilation,erosion,closing,opening,blur}
in_images [in_images ...] out_image
Performs an operation on a list of images. The supported operations are
listed below.
This script is loading all images in memory, will often crash after a few
hundred images.
Some operations such as multiplication or addition accept float value as
parameters instead of images.
> scil_volume_math.py multiplication img.nii.gz 10 mult_10.nii.gz
Formerly: scil_image_math.py
lower_threshold: IMG THRESHOLD
All values below the threshold will be set to zero.
All values above the threshold will be set to one.
upper_threshold: IMG THRESHOLD
All values below the threshold will be set to one.
All values above the threshold will be set to zero.
Equivalent to lower_threshold followed by an inversion.
lower_threshold_eq: IMG THRESHOLD
All values below the threshold will be set to zero.
All values above or equal the threshold will be set to one.
upper_threshold_eq: IMG THRESHOLD
All values below or equal the threshold will be set to one.
All values above the threshold will be set to zero.
Equivalent to lower_threshold followed by an inversion.
lower_threshold_otsu: IMG
All values below or equal to the Otsu threshold will be set to zero.
All values above the Otsu threshold will be set to one.
upper_threshold_otsu: IMG
All values below the Otsu threshold will be set to one.
All values above or equal to the Otsu threshold will be set to zero.
Equivalent to lower_threshold_otsu followed by an inversion.
lower_clip: IMG THRESHOLD
All values below the threshold will be set to threshold.
upper_clip: IMG THRESHOLD
All values above the threshold will be set to threshold.
absolute_value: IMG
All negative values will become positive.
round: IMG
Round all decimal values to the closest integer.
ceil: IMG
Ceil all decimal values to the next integer.
floor: IMG
Floor all decimal values to the previous integer.
normalize_sum: IMG
Normalize the image so the sum of all values is one.
normalize_max: IMG
Normalize the image so the maximum value is one.
log_10: IMG
Apply a log (base 10) to all non zeros values of an image.
log_e: IMG
Apply a natural log to all non zeros values of an image.
convert: IMG
Perform no operation, but simply change the data type.
invert: IMG
Operation on binary image to interchange 0s and 1s in a binary mask.
addition: IMGs
Add multiple images together.
subtraction: IMG_1 IMG_2
Subtract first image by the second (IMG_1 - IMG_2).
multiplication: IMGs
Multiply multiple images together (danger of underflow and overflow)
division: IMG_1 IMG_2
Divide first image by the second (danger of underflow and overflow)
Ignore zeros values, excluded from the operation.
mean: IMGs
Compute the mean of images.
If a single 4D image is provided, average along the last dimension.
std: IMGs
Compute the standard deviation average of multiple images.
If a single 4D image is provided, compute the STD along the last
dimension.
correlation: IMGs
Compute the correlation average of multiple images.
union: IMGs
Operation on binary image to keep voxels, that are non-zero, in at
least one file.
intersection: IMGs
Operation on binary image to keep the voxels, that are non-zero,
are present in all files.
difference: IMG_1 IMG_2
Operation on binary image to keep voxels from the first file that are
not in the second file (non-zeros).
concatenate: IMGs
Concatenate a list of 3D and 4D images into a single 4D image.
dilation: IMG, VALUE
Binary morphological operation to spatially extend the values of an
image to their neighbors. VALUE is in voxels.
erosion: IMG, VALUE
Binary morphological operation to spatially shrink the volume contained
in a binary image. VALUE is in voxels.
closing: IMG, VALUE
Binary morphological operation, dilation followed by an erosion.
opening: IMG, VALUE
Binary morphological operation, erosion followed by a dilation.
blur: IMG, VALUE
Apply a gaussian blur to a single image.
positional arguments:
{lower_threshold,upper_threshold,lower_threshold_eq,upper_threshold_eq,lower_threshold_otsu,upper_threshold_otsu,lower_clip,upper_clip,absolute_value,round,ceil,floor,normalize_sum,normalize_max,log_10,log_e,convert,invert,addition,subtraction,multiplication,division,mean,std,correlation,union,intersection,difference,concatenate,dilation,erosion,closing,opening,blur}
The type of operation to be performed on the images.
in_images The list of image files or parameters.
out_image Output image path.
options:
-h, --help show this help message and exit
--data_type DATA_TYPE
Data type of the output image. Use the format: uint8, int16, int/float32, int/float64.
--exclude_background Does not affect the background of the original images.
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
-f Force overwriting of the output files.