Source code for asap.intensity_correction.schemas

from argschema.fields import Str, Float, Int, Bool, OutputDir
from asap.module.schemas import StackTransitionParameters


class MakeMedianParams(StackTransitionParameters):
    file_prefix = Str(
        required=False, default="Median",
        description='File prefix for median image file that is saved')
    output_directory = Str(
        required=True,
        description='Output Directory for saving median image')
    num_images = Int(
        required=False, default=-1,
        description=("Number of images to randomly "
                     "subsample to generate median"))


class MultIntensityCorrParams(StackTransitionParameters):
    correction_stack = Str(
        required=True,
        description='Correction stack (usually median stack for AT data)')
    output_directory = OutputDir(
        required=True,
        description='Directory for storing Images')
    # TODO add create_stack metadata
    cycle_number = Int(
        required=False, default=2,
        description="what cycleNumber to upload for output_stack on render")
    cycle_step_number = Int(
        required=False, default=1,
        description=("what cycleStepNumber to upload "
                     "for output_stack on render"))
    clip = Bool(
        required=False, default=True,
        description="whether to clip values")
    scale_factor = Float(
        required=False, default=1.0,
        description="scaling value")
    clip_min = Int(
        required=False, default=0,
        description='Min Clip value')
    clip_max = Int(
        required=False, default=65535,
        description='Max Clip value')