# -*- coding: utf-8 -*-
# -*- coding: utf8 -*-
"""Autogenerated file - DO NOT EDIT
If you spot a bug, please report it on the mailing list and/or change the generator."""

import os

from ...base import (
    CommandLine,
    CommandLineInputSpec,
    SEMLikeCommandLine,
    TraitedSpec,
    File,
    Directory,
    traits,
    isdefined,
    InputMultiPath,
    OutputMultiPath,
)


class HistogramMatchingFilterInputSpec(CommandLineInputSpec):
    inputVolume = File(
        desc="The Input image to be computed for statistics",
        exists=True,
        argstr="--inputVolume %s",
    )
    referenceVolume = File(
        desc="The Input image to be computed for statistics",
        exists=True,
        argstr="--referenceVolume %s",
    )
    outputVolume = traits.Either(
        traits.Bool,
        File(),
        hash_files=False,
        desc="Output Image File Name",
        argstr="--outputVolume %s",
    )
    referenceBinaryVolume = File(
        desc="referenceBinaryVolume", exists=True, argstr="--referenceBinaryVolume %s"
    )
    inputBinaryVolume = File(
        desc="inputBinaryVolume", exists=True, argstr="--inputBinaryVolume %s"
    )
    numberOfMatchPoints = traits.Int(
        desc=" number of histogram matching points", argstr="--numberOfMatchPoints %d"
    )
    numberOfHistogramBins = traits.Int(
        desc=" number of histogram bin", argstr="--numberOfHistogramBins %d"
    )
    writeHistogram = traits.Str(
        desc=" decide if histogram data would be written with prefixe of the file name",
        argstr="--writeHistogram %s",
    )
    histogramAlgorithm = traits.Enum(
        "OtsuHistogramMatching",
        desc=" histogram algrithm selection",
        argstr="--histogramAlgorithm %s",
    )
    verbose = traits.Bool(
        desc=" verbose mode running for debbuging", argstr="--verbose "
    )


class HistogramMatchingFilterOutputSpec(TraitedSpec):
    outputVolume = File(desc="Output Image File Name", exists=True)


class HistogramMatchingFilter(SEMLikeCommandLine):
    """title: Write Out Image Intensities

    category: BRAINS.Utilities

    description: For Analysis

    version: 0.1

    contributor: University of Iowa Department of Psychiatry, http:://www.psychiatry.uiowa.edu
    """

    input_spec = HistogramMatchingFilterInputSpec
    output_spec = HistogramMatchingFilterOutputSpec
    _cmd = " HistogramMatchingFilter "
    _outputs_filenames = {"outputVolume": "outputVolume.nii"}
    _redirect_x = False


class GenerateEdgeMapImageInputSpec(CommandLineInputSpec):
    inputMRVolumes = InputMultiPath(
        File(exists=True),
        desc="List of input structural MR volumes to create the maximum edgemap",
        argstr="--inputMRVolumes %s...",
    )
    inputMask = File(
        desc="Input mask file name. If set, image histogram percentiles will be calculated within the mask",
        exists=True,
        argstr="--inputMask %s",
    )
    minimumOutputRange = traits.Int(
        desc="Map lower quantile and below to minimum output range. It should be a small number greater than zero. Default is 1",
        argstr="--minimumOutputRange %d",
    )
    maximumOutputRange = traits.Int(
        desc="Map upper quantile and above to maximum output range. Default is 255 that is the maximum range of unsigned char",
        argstr="--maximumOutputRange %d",
    )
    lowerPercentileMatching = traits.Float(
        desc="Map lower quantile and below to minOutputRange. It should be a value between zero and one",
        argstr="--lowerPercentileMatching %f",
    )
    upperPercentileMatching = traits.Float(
        desc="Map upper quantile and above to maxOutputRange. It should be a value between zero and one",
        argstr="--upperPercentileMatching %f",
    )
    outputEdgeMap = traits.Either(
        traits.Bool,
        File(),
        hash_files=False,
        desc="output edgemap file name",
        argstr="--outputEdgeMap %s",
    )
    outputMaximumGradientImage = traits.Either(
        traits.Bool,
        File(),
        hash_files=False,
        desc="output gradient image file name",
        argstr="--outputMaximumGradientImage %s",
    )
    numberOfThreads = traits.Int(
        desc="Explicitly specify the maximum number of threads to use.",
        argstr="--numberOfThreads %d",
    )


class GenerateEdgeMapImageOutputSpec(TraitedSpec):
    outputEdgeMap = File(desc="(required) output file name", exists=True)
    outputMaximumGradientImage = File(
        desc="output gradient image file name", exists=True
    )


class GenerateEdgeMapImage(SEMLikeCommandLine):
    """title: GenerateEdgeMapImage

    category: BRAINS.Utilities

    description: Automatic edgemap generation for edge-guided super-resolution reconstruction

    version: 1.0

    contributor: Ali Ghayoor
    """

    input_spec = GenerateEdgeMapImageInputSpec
    output_spec = GenerateEdgeMapImageOutputSpec
    _cmd = " GenerateEdgeMapImage "
    _outputs_filenames = {
        "outputEdgeMap": "outputEdgeMap",
        "outputMaximumGradientImage": "outputMaximumGradientImage",
    }
    _redirect_x = False


class GeneratePurePlugMaskInputSpec(CommandLineInputSpec):
    inputImageModalities = InputMultiPath(
        File(exists=True),
        desc="List of input image file names to create pure plugs mask",
        argstr="--inputImageModalities %s...",
    )
    threshold = traits.Float(
        desc="threshold value to define class membership", argstr="--threshold %f"
    )
    numberOfSubSamples = InputMultiPath(
        traits.Int,
        desc="Number of continous index samples taken at each direction of lattice space for each plug volume",
        sep=",",
        argstr="--numberOfSubSamples %s",
    )
    outputMaskFile = traits.Either(
        traits.Bool,
        File(),
        hash_files=False,
        desc="Output binary mask file name",
        argstr="--outputMaskFile %s",
    )


class GeneratePurePlugMaskOutputSpec(TraitedSpec):
    outputMaskFile = File(desc="(required) Output binary mask file name", exists=True)


class GeneratePurePlugMask(SEMLikeCommandLine):
    """title: GeneratePurePlugMask

    category: BRAINS.Utilities

    description: This program gets several modality image files and returns a binary mask that defines the pure plugs

    version: 1.0

    contributor: Ali Ghayoor
    """

    input_spec = GeneratePurePlugMaskInputSpec
    output_spec = GeneratePurePlugMaskOutputSpec
    _cmd = " GeneratePurePlugMask "
    _outputs_filenames = {"outputMaskFile": "outputMaskFile"}
    _redirect_x = False