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.
(Otsu's method is an algorithm to perform automatic matrix thresholding
of the background.)
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
Computes the correlation of the 3x3x3 neighborhood of each voxel, for
all pair of input matrices. The final matrix is the average correlation
(through all pairs).
For a given pair of matrices
- Background is considered as 0. May lead to very high correlations
close to the border of the background regions, or very poor ones if the
background in both matrices differ.
- Images are zero-padded. For the same reason as higher, may lead to
very high correlations if you have data close to the border of the
matrix.
- NaN values (if a voxel's neighborhood is entirely uniform; std 0) are
replaced by
- 0 if at least one neighborhood was entirely containing background.
- 1 if the voxel's neighborhoods are uniform in both matrices
- 0 if the voxel's neighborhoods is uniform in one matrix, but not
the other.
UPDATE AS OF VERSION 2.0: Random noise was previously added in the
process to help avoid NaN values. Now replaced by either 0 or 1 as
explained above.
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.