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DOC: Update on InputSpec and OutputSpec descriptions
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@pdedumast
pdedumast committed Oct 30, 2020
1 parent 04f0d13 commit 95ac456
Showing 1 changed file with 41 additions and 51 deletions.
92 changes: 41 additions & 51 deletions pymialsrtk/interfaces/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,15 +49,13 @@

class BtkNLMDenoisingInputSpec(BaseInterfaceInputSpec):
bids_dir = Directory(desc='BIDS root directory', mandatory=True, exists=True)
in_file = File(desc='Input image', mandatory=True)
in_mask = File(desc='Input mask', mandatory=False)
out_postfix = traits.Str("_nlm", desc='Suffix to be added to in_file', usedefault=True)
weight = traits.Float(0.1, desc='NLM weight (0.1 by default)', usedefault=True)

in_file = File(desc='Input image filename', mandatory=True)
in_mask = File(desc='Input mask filename', mandatory=False)
out_postfix = traits.Str("_nlm", desc='Suffix to be added to input image filename to construst denoised output filename', usedefault=True)
weight = traits.Float(0.1, desc='NLM smoothing parameter (0.1 by default)', usedefault=True)

class BtkNLMDenoisingOutputSpec(TraitedSpec):
out_file = File(desc='Denoised image')

out_file = File(desc='Output denoised image')

class BtkNLMDenoising(BaseInterface):
"""
Expand Down Expand Up @@ -94,7 +92,6 @@ class BtkNLMDenoising(BaseInterface):
>>> nlmDenoise.inputs.in_mask = 'my_mask.nii.gz'
>>> nlmDenoise.inputs.weight = 0.2
>>> nlmDenoise.run() # doctest: +SKIP
"""

input_spec = BtkNLMDenoisingInputSpec
Expand Down Expand Up @@ -127,14 +124,14 @@ def _list_outputs(self):

class MultipleBtkNLMDenoisingInputSpec(BaseInterfaceInputSpec):
bids_dir = Directory(desc='BIDS root directory', mandatory=True, exists=True)
input_images = InputMultiPath(File(desc='files to be denoised', mandatory=True))
input_masks = InputMultiPath(File(desc='mask of files to be denoised', mandatory=False))
weight = traits.Float(0.1, desc='NLM weight (0.1 by default)', usedefault=True)
out_postfix = traits.Str("_nlm", desc='Suffixe to be added to input_images',usedefault=True)
input_images = InputMultiPath(File(desc='Input image filenames to be denoised', mandatory=True))
input_masks = InputMultiPath(File(desc='Input mask filenames', mandatory=False))
weight = traits.Float(0.1, desc='NLM smoothing parameter (0.1 by default)', usedefault=True)
out_postfix = traits.Str("_nlm", desc='Suffix to be added to input image filenames to construst denoised output filenames',usedefault=True)
stacksOrder = traits.List(desc='To_be_completed', mandatory=False)

class MultipleBtkNLMDenoisingOutputSpec(TraitedSpec):
output_images = OutputMultiPath(File())
output_images = OutputMultiPath(File(desc='Output denoised images'))

class MultipleBtkNLMDenoising(BaseInterface):
"""
Expand Down Expand Up @@ -232,17 +229,14 @@ def _list_outputs(self):
# Slice intensity correction
#############################


class MialsrtkCorrectSliceIntensityInputSpec(BaseInterfaceInputSpec):
bids_dir = Directory(desc='BIDS root directory', mandatory=True, exists=True)
in_file = File(desc='Input image', mandatory=True)
in_mask = File(desc='Input mask', mandatory=False)
out_postfix = traits.Str("", desc='Suffixe to be added to in_file', usedefault=True)

in_file = File(desc='Input image filename', mandatory=True)
in_mask = File(desc='Input mask filename', mandatory=False)
out_postfix = traits.Str("", desc='Suffix to be added to input image file to construct corrected output filename', usedefault=True)

class MialsrtkCorrectSliceIntensityOutputSpec(TraitedSpec):
out_file = File(desc='Corrected slice intensities')

out_file = File(desc='Output image with corrected slice intensities')

class MialsrtkCorrectSliceIntensity(BaseInterface):
"""
Expand Down Expand Up @@ -298,10 +292,10 @@ def _list_outputs(self):

class MultipleMialsrtkCorrectSliceIntensityInputSpec(BaseInterfaceInputSpec):
bids_dir = Directory(desc='BIDS root directory', mandatory=True, exists=True)
input_images = InputMultiPath(File(desc='files to be corrected for intensity', mandatory=True))
input_masks = InputMultiPath(File(desc='mask of files to be corrected for intensity', mandatory=False))
out_postfix = traits.Str("", desc='Suffixe to be added to input_images',usedefault=True)
stacksOrder = traits.List(mandatory=False)
input_images = InputMultiPath(File(desc='Input image filenames to be corrected for slice intensity', mandatory=True))
input_masks = InputMultiPath(File(desc='Input mask filenames', mandatory=False))
out_postfix = traits.Str("", desc='Suffix to be added to input image filenames to construct corrected output filenames',usedefault=True)
stacksOrder = traits.List(desc='To_be_completed', mandatory=False)

class MultipleMialsrtkCorrectSliceIntensityOutputSpec(TraitedSpec):
output_images = OutputMultiPath(File())
Expand Down Expand Up @@ -393,12 +387,12 @@ class MialsrtkSliceBySliceN4BiasFieldCorrectionInputSpec(BaseInterfaceInputSpec)
bids_dir = Directory(desc='BIDS root directory', mandatory=True, exists=True)
in_file = File(desc='Input image', mandatory=True)
in_mask = File(desc='Input mask', mandatory=True)
out_im_postfix = traits.Str("_bcorr", desc='Suffixe to be added to N4 bias correced in_file ', usedefault=True)
out_fld_postfix = traits.Str("_n4bias", desc='Suffixe to be added to the bias', usedefault=True)
out_im_postfix = traits.Str("_bcorr", desc='Suffix to be added to input image filename to construct corrected output filename', usedefault=True)
out_fld_postfix = traits.Str("_n4bias", desc='Suffix to be added to input image filename to construct output bias field filename', usedefault=True)

class MialsrtkSliceBySliceN4BiasFieldCorrectionOutputSpec(TraitedSpec):
out_im_file = File(desc='Corrected slice by slice from N4 bias field')
out_fld_file = File(desc='slice by slice N4 bias field')
out_im_file = File(desc='Filename of corrected output image from N4 bias field (slice by slice).')
out_fld_file = File(desc='Filename bias field extracted slice by slice from input image.')

class MialsrtkSliceBySliceN4BiasFieldCorrection(BaseInterface):
"""
Expand Down Expand Up @@ -472,9 +466,9 @@ class MultipleMialsrtkSliceBySliceN4BiasFieldCorrectionInputSpec(BaseInterfaceIn
bids_dir = Directory(desc='BIDS root directory', mandatory=True, exists=True)
input_images = InputMultiPath(File(desc='files to be corrected for intensity', mandatory=True))
input_masks = InputMultiPath(File(desc='mask of files to be corrected for intensity', mandatory=True))
out_im_postfix = traits.Str("_bcorr", desc='Suffixe to be added to the bias corrected input_images', usedefault=True)
out_fld_postfix = traits.Str("_n4bias", desc='Suffixe to be added to the bias', usedefault=True)
stacksOrder = traits.List(madatory=False)
out_im_postfix = traits.Str("_bcorr", desc='Suffix to be added to input image filenames to construct corrected output filenames', usedefault=True)
out_fld_postfix = traits.Str("_n4bias", desc='Suffix to be added to input image filenames to construct output bias field filenames', usedefault=True)
stacksOrder = traits.List(desc='To_be_completed', mandatory=False)

class MultipleMialsrtkSliceBySliceN4BiasFieldCorrectionOutputSpec(TraitedSpec):
output_images = OutputMultiPath(File())
Expand Down Expand Up @@ -642,7 +636,7 @@ class MultipleMialsrtkSliceBySliceCorrectBiasFieldInputSpec(BaseInterfaceInputSp
input_masks = InputMultiPath(File(desc='mask of files to be corrected for intensity', mandatory=True))
input_fields = InputMultiPath(File(desc='field to remove', mandatory=True))
out_im_postfix = traits.Str("_bcorr", desc='Suffixe to be added to bias field corrected input_images', usedefault=True)
stacksOrder = traits.List(mandatory=False)
stacksOrder = traits.List(desc='To_be_completed', mandatory=False)

class MultipleMialsrtkSliceBySliceCorrectBiasFieldOutputSpec(TraitedSpec):
output_images = OutputMultiPath(File())
Expand Down Expand Up @@ -738,13 +732,12 @@ def _list_outputs(self):
# Intensity standardization
#############################


class MialsrtkIntensityStandardizationInputSpec(BaseInterfaceInputSpec):
bids_dir = Directory(desc='BIDS root directory', mandatory=True, exists=True)
input_images = InputMultiPath(File(desc='files to be corrected for intensity', mandatory=True))
out_postfix = traits.Str("", desc='Suffixe to be added to intensity corrected input_images', usedefault=True)
out_postfix = traits.Str("", desc='Suffix to be added to intensity corrected input_images', usedefault=True)
in_max = traits.Float(desc='Maximal intensity',usedefault=False)
stacksOrder = traits.List(desc='To_be_completed',mandatory=False) # ToDo: Can be removed -> Also in pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline !!!
stacksOrder = traits.List(desc='To_be_completed', mandatory=False) # ToDo: Can be removed -> Also in pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline !!!

class MialsrtkIntensityStandardizationOutputSpec(TraitedSpec):
output_images = OutputMultiPath(File())
Expand Down Expand Up @@ -776,7 +769,7 @@ class MialsrtkIntensityStandardization(BaseInterface):
>>> intensityStandardization.inputs.input_images = ['image1.nii.gz','image2.nii.gz']
>>> intensityStandardization.run() # doctest: +SKIP
"""

input_spec = MialsrtkIntensityStandardizationInputSpec
output_spec = MialsrtkIntensityStandardizationOutputSpec

Expand Down Expand Up @@ -811,10 +804,10 @@ def _list_outputs(self):

class MialsrtkHistogramNormalizationInputSpec(BaseInterfaceInputSpec):
bids_dir = Directory(desc='BIDS root directory', mandatory=True, exists=True)
input_images = InputMultiPath(File(desc='files to be HistNorm', mandatory=True))
input_masks = InputMultiPath(File(desc='mask of files to be HistNorm', mandatory=False))
out_postfix = traits.Str("_histnorm", desc='Suffixe to be added to HistNorm input_images', usedefault=True)
stacksOrder = traits.List(desc='To_be_completed',mandatory=False)
input_images = InputMultiPath(File(desc='Input image filenames to be normalized', mandatory=True))
input_masks = InputMultiPath(File(desc='Input mask filenames', mandatory=False))
out_postfix = traits.Str("_histnorm", desc='Suffix to be added to normalized input image filenames to construct ouptut normalized image filenames', usedefault=True)
stacksOrder = traits.List(desc='To_be_completed', mandatory=False)


class MialsrtkHistogramNormalizationOutputSpec(TraitedSpec):
Expand Down Expand Up @@ -912,15 +905,13 @@ def _list_outputs(self):

class MialsrtkMaskImageInputSpec(BaseInterfaceInputSpec):
bids_dir = Directory(desc='BIDS root directory',mandatory=True,exists=True)
in_file = File(desc='Input image',mandatory=True)
in_mask = File(desc='Input mask',mandatory=True)
out_im_postfix = traits.Str("", desc='Suffixe to be added to masked in_file', usedefault=True)

in_file = File(desc='Input image filename to be masked',mandatory=True)
in_mask = File(desc='Input mask filename',mandatory=True)
out_im_postfix = traits.Str("", desc='Suffix to be added to masked in_file', usedefault=True)

class MialsrtkMaskImageOutputSpec(TraitedSpec):
out_im_file = File(desc='Masked image')


class MialsrtkMaskImage(BaseInterface):
"""
Runs the MIAL SRTK mask image module.
Expand Down Expand Up @@ -975,13 +966,13 @@ def _list_outputs(self):

class MultipleMialsrtkMaskImageInputSpec(BaseInterfaceInputSpec):
bids_dir = Directory(desc='BIDS root directory', mandatory=True, exists=True)
input_images = InputMultiPath(File(desc='files to be corrected for intensity', mandatory=True))
input_masks = InputMultiPath(File(desc='mask of files to be corrected for intensity', mandatory=True))
out_im_postfix = traits.Str("", desc='Suffixe to be added to masked input_images', usedefault=True)
stacksOrder = traits.List(mandatory=False)
input_images = InputMultiPath(File(desc='Input image filenames to be corrected for intensity', mandatory=True))
input_masks = InputMultiPath(File(desc='Input mask filenames ', mandatory=True))
out_im_postfix = traits.Str("", desc='Suffix to be added to masked input_images', usedefault=True)
stacksOrder = traits.List(desc='To_be_completed', mandatory=False)

class MultipleMialsrtkMaskImageOutputSpec(TraitedSpec):
output_images = OutputMultiPath(File())
output_images = OutputMultiPath(File(desc='Output masked image filenames'))

class MultipleMialsrtkMaskImage(BaseInterface):
"""
Expand Down Expand Up @@ -1022,7 +1013,6 @@ class MultipleMialsrtkMaskImage(BaseInterface):
See also
------------
pymialsrtk.interfaces.preprocess.MialsrtkMaskImage
"""

input_spec = MultipleMialsrtkMaskImageInputSpec
Expand Down

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