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}
in_matrices [in_matrices ...] out_matrix
Performs an operation on a list of matrices. The supported operations are
listed below.
Some operations such as multiplication or addition accept float value as
parameters instead of matrices.
> scil_connectivity_math.py multiplication mat.npy 10 mult_10.npy
lower_threshold: MAT THRESHOLD
All values below the threshold will be set to zero.
All values above the threshold will be set to one.
upper_threshold: MAT 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: MAT 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: MAT 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: MAT
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: MAT
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: MAT THRESHOLD
All values below the threshold will be set to threshold.
upper_clip: MAT THRESHOLD
All values above the threshold will be set to threshold.
absolute_value: MAT
All negative values will become positive.
round: MAT
Round all decimal values to the closest integer.
ceil: MAT
Ceil all decimal values to the next integer.
floor: MAT
Floor all decimal values to the previous integer.
normalize_sum: MAT
Normalize the matrix so the sum of all values is one.
normalize_max: MAT
Normalize the matrix so the maximum value is one.
log_10: MAT
Apply a log (base 10) to all non zeros values of an matrix.
log_e: MAT
Apply a natural log to all non zeros values of an matrix.
convert: MAT
Perform no operation, but simply change the data type.
invert: MAT
Operation on binary matrix to interchange 0s and 1s in a binary mask.
addition: MATs
Add multiple matrices together.
subtraction: MAT_1 MAT_2
Subtract first matrix by the second (MAT_1 - MAT_2).
multiplication: MATs
Multiply multiple matrices together (danger of underflow and overflow)
division: MAT_1 MAT_2
Divide first matrix by the second (danger of underflow and overflow)
Ignore zeros values, excluded from the operation.
mean: MATs
Compute the mean of matrices.
If a single 4D matrix is provided, average along the last dimension.
std: MATs
Compute the standard deviation average of multiple matrices.
If a single 4D matrix is provided, compute the STD along the last
dimension.
correlation: MATs
Compute the correlation average of multiple matrices.
union: MATs
Operation on binary matrix to keep voxels, that are non-zero, in at
least one file.
intersection: MATs
Operation on binary matrix to keep the voxels, that are non-zero,
are present in all files.
difference: MAT_1 MAT_2
Operation on binary matrix to keep voxels from the first file that are
not in the second file (non-zeros).
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}
The type of operation to be performed on the matrices.
in_matrices The list of matrices files or parameters.
out_matrix Output matrix path.
options:
-h, --help show this help message and exit
--data_type DATA_TYPE
Data type of the output image. Use the format: uint8, float16, int32.
--exclude_background Does not affect the background of the original matrices.
-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.