Batch Processing: Transformation¶
mp-transformation.py
can be run from the command line after setting parameters in mp-transformation-config.json
. When you run the script, you only need to provide the path to the config file as an argument
$ python mp-transformation.py "C:\\path\\to\\mp-transformation-config.json"
In addition to the parameters described in Parameter Reference, mp-transformation-config.json
requires a set of additional parameters:
-
rootdir
¶ Required: String specifying the complete path to a directory where an output folder should be created
-
expname
¶ Required: String specifying the experiment name that will be incorporated into output files
-
c1-dir
¶ Required: String specifying the path to the directory containing the
_Probabilities.files
for the structural channel
-
c1-key
¶ Required: String that will serve as a key for the structural channel and will name the output files
-
twoD
¶ A boolean value that specifies, which PCA transformation functions will be used.
True
:brain.calculate_pca_median_2d()
andbrain.pca_transform_2d()
will be used to hold one axis constant, while the other two are realigned with PCAFalse
:brain.calculate_pca_median()
andbrain.pca_transform_3d()
will be used to transform and realign samples in all three dimensions
API¶
-
deltascope.mpTransformation.
check_nums
(P)¶ Check that the numbers of files selected by the same list index match Raises an error if file numbers are mismatched
:param
paramClass
P: Object containing all variables from config file
-
class
deltascope.mpTransformation.
paramsClass
(path)¶ A class to read and validate parameters for multiprocessing transformation. Validated parameters can be read as attributes of the object
-
add_outdir
(path)¶ Add out directory as an attribute of the class
Parameters: path (str) – Complete path to the output directory
-
check_config
(D, path)¶ Check that each parameter in the config file is correct and raise an error if it isn’t
Parameters: - D (dict) – Dictionary containing parameters from the config file
- path (str) – Complete filepath to the config file
-
-
deltascope.mpTransformation.
process
(num, P=None)¶ Run through the processing steps for a single sample through saving psi files
Parameters: num (int) – Index of the file that is currently being processed :param
paramClass
P: Object containing all variables from config file