Python CLI changes

bin/dwi2response

@@ -33,10 +33,10 @@ def usage(cmdline): #pylint: disable=unused-variable
 
   # General options
   common_options = cmdline.add_argument_group('General dwi2response options')
-  common_options.add_argument('-mask', help='Provide an initial mask for response voxel selection')
-  common_options.add_argument('-voxels', help='Output an image showing the final voxel selection(s)')
-  common_options.add_argument('-shells', help='The b-value(s) to use in response function estimation (comma-separated list in case of multiple b-values, b=0 must be included explicitly)')
-  common_options.add_argument('-lmax', help='The maximum harmonic degree(s) for response function estimation (comma-separated list in case of multiple b-values)')
+  common_options.add_argument('-mask', type=app.Parser.ImageIn(), metavar='image', help='Provide an initial mask for response voxel selection')
+  common_options.add_argument('-voxels', type=app.Parser.ImageOut(), metavar='image', help='Output an image showing the final voxel selection(s)')
+  common_options.add_argument('-shells', type=app.Parser.SequenceFloat(), help='The b-value(s) to use in response function estimation (comma-separated list in case of multiple b-values, b=0 must be included explicitly)')
+  common_options.add_argument('-lmax', type=app.Parser.SequenceInt(), help='The maximum harmonic degree(s) for response function estimation (comma-separated list in case of multiple b-values)')
   app.add_dwgrad_import_options(cmdline)
 
   # Import the command-line settings for all algorithms found in the relevant directory
@@ -62,7 +62,7 @@ def execute(): #pylint: disable=unused-variable
   # Sanitise some inputs, and get ready for data import
   if app.ARGS.lmax:
     try:
-      lmax = [ int(x) for x in app.ARGS.lmax.split(',') ]
+      lmax = app.ARGS.lmax
       if any(lmax_value%2 for lmax_value in lmax):
         raise MRtrixError('Value of lmax must be even')
     except ValueError as exception:
@@ -72,12 +72,12 @@ def execute(): #pylint: disable=unused-variable
   shells_option = ''
   if app.ARGS.shells:
     try:
-      shells_values = [ int(round(float(x))) for x in app.ARGS.shells.split(',') ]
+      shells_values = [ int(round(x)) for x in app.ARGS.shells ]
     except ValueError as exception:
       raise MRtrixError('-shells option should provide a comma-separated list of b-values') from exception
     if alg.needs_single_shell() and not len(shells_values) == 1:
       raise MRtrixError('Can only specify a single b-value shell for single-shell algorithms')
-    shells_option = ' -shells ' + app.ARGS.shells
+    shells_option = ' -shells ' + ','.join(str(item) for item in app.ARGS.shells)
   singleshell_option = ''
   if alg.needs_single_shell():
     singleshell_option = ' -singleshell -no_bzero'

bin/dwibiascorrect

@@ -26,8 +26,8 @@ def usage(cmdline): #pylint: disable=unused-variable
                           'More information on mask derivation from DWI data can be found at the following link: \n'
                           'https://mrtrix.readthedocs.io/en/' + _version.__tag__ + '/dwi_preprocessing/masking.html')
   common_options = cmdline.add_argument_group('Options common to all dwibiascorrect algorithms')
-  common_options.add_argument('-mask', metavar='image', help='Manually provide a mask image for bias field estimation')
-  common_options.add_argument('-bias', metavar='image', help='Output the estimated bias field')
+  common_options.add_argument('-mask', type=app.Parser.ImageIn(), metavar='image', help='Manually provide an input mask image for bias field estimation')
+  common_options.add_argument('-bias', type=app.Parser.ImageOut(), metavar='image', help='Output an image containing the estimated bias field')
   app.add_dwgrad_import_options(cmdline)
 
   # Import the command-line settings for all algorithms found in the relevant directory

bin/dwicat

@@ -22,16 +22,18 @@ import json, shutil
 
 
 def usage(cmdline): #pylint: disable=unused-variable
+  from mrtrix3 import app
+
   cmdline.set_author('Lena Dorfschmidt (ld548@cam.ac.uk) and Jakub Vohryzek (jakub.vohryzek@queens.ox.ac.uk) and Robert E. Smith (robert.smith@florey.edu.au)')
   cmdline.set_synopsis('Concatenating multiple DWI series accounting for differential intensity scaling')
   cmdline.add_description('This script concatenates two or more 4D DWI series, accounting for the '
                           'fact that there may be differences in intensity scaling between those series. '
                           'This intensity scaling is corrected by determining scaling factors that will '
                           'make the overall image intensities in the b=0 volumes of each series approximately '
                           'equivalent.')
-  cmdline.add_argument('inputs', nargs='+', help='Multiple input diffusion MRI series')
-  cmdline.add_argument('output', help='The output image series (all DWIs concatenated)')
-  cmdline.add_argument('-mask', metavar='image', help='Provide a binary mask within which image intensities will be matched')
+  cmdline.add_argument('inputs', nargs='+', type=app.Parser.ImageIn(), help='Multiple input diffusion MRI series')
+  cmdline.add_argument('output', type=app.Parser.ImageOut(), help='The output image series (all DWIs concatenated)')
+  cmdline.add_argument('-mask', metavar='image', type=app.Parser.ImageIn(), help='Provide a binary mask within which image intensities will be matched')
 
 
 

bin/dwifslpreproc

@@ -50,27 +50,27 @@ def usage(cmdline): #pylint: disable=unused-variable
   cmdline.add_citation('Andersson, J. L. R.; Graham, M. S.; Zsoldos, E. & Sotiropoulos, S. N. Incorporating outlier detection and replacement into a non-parametric framework for movement and distortion correction of diffusion MR images. NeuroImage, 2016, 141, 556-572', condition='If including "--repol" in -eddy_options input', is_external=True)
   cmdline.add_citation('Andersson, J. L. R.; Graham, M. S.; Drobnjak, I.; Zhang, H.; Filippini, N. & Bastiani, M. Towards a comprehensive framework for movement and distortion correction of diffusion MR images: Within volume movement. NeuroImage, 2017, 152, 450-466', condition='If including "--mporder" in -eddy_options input', is_external=True)
   cmdline.add_citation('Bastiani, M.; Cottaar, M.; Fitzgibbon, S.P.; Suri, S.; Alfaro-Almagro, F.; Sotiropoulos, S.N.; Jbabdi, S.; Andersson, J.L.R. Automated quality control for within and between studies diffusion MRI data using a non-parametric framework for movement and distortion correction. NeuroImage, 2019, 184, 801-812', condition='If using -eddyqc_text or -eddyqc_all option and eddy_quad is installed', is_external=True)
-  cmdline.add_argument('input',  help='The input DWI series to be corrected')
-  cmdline.add_argument('output', help='The output corrected image series')
-  cmdline.add_argument('-json_import', metavar=('file'), help='Import image header information from an associated JSON file (may be necessary to determine phase encoding information)')
+  cmdline.add_argument('input', type=app.Parser.ImageIn(), help='The input DWI series to be corrected')
+  cmdline.add_argument('output', type=app.Parser.ImageOut(), help='The output corrected image series')
+  cmdline.add_argument('-json_import', type=app.Parser.FileIn(), metavar=('file'), help='Import image header information from an associated JSON file (may be necessary to determine phase encoding information)')
   pe_options = cmdline.add_argument_group('Options for manually specifying the phase encoding of the input DWIs')
   pe_options.add_argument('-pe_dir', metavar=('PE'), help='Manually specify the phase encoding direction of the input series; can be a signed axis number (e.g. -0, 1, +2), an axis designator (e.g. RL, PA, IS), or NIfTI axis codes (e.g. i-, j, k)')
-  pe_options.add_argument('-readout_time', metavar=('time'), type=float, help='Manually specify the total readout time of the input series (in seconds)')
+  pe_options.add_argument('-readout_time', metavar='time', type=float, help='Manually specify the total readout time of the input series (in seconds)')
   distcorr_options = cmdline.add_argument_group('Options for achieving correction of susceptibility distortions')
-  distcorr_options.add_argument('-se_epi', metavar=('image'), help='Provide an additional image series consisting of spin-echo EPI images, which is to be used exclusively by topup for estimating the inhomogeneity field (i.e. it will not form part of the output image series)')
+  distcorr_options.add_argument('-se_epi', type=app.Parser.ImageIn(), metavar='image', help='Provide an additional image series consisting of spin-echo EPI images, which is to be used exclusively by topup for estimating the inhomogeneity field (i.e. it will not form part of the output image series)')
   distcorr_options.add_argument('-align_seepi', action='store_true', help='Achieve alignment between the SE-EPI images used for inhomogeneity field estimation, and the DWIs (more information in Description section)')
-  distcorr_options.add_argument('-topup_options', metavar=('" TopupOptions"'), help='Manually provide additional command-line options to the topup command (provide a string within quotation marks that contains at least one space, even if only passing a single command-line option to topup)')
-  distcorr_options.add_argument('-topup_files', metavar=('prefix'), help='Provide files generated by prior execution of the FSL "topup" command to be utilised by eddy')
+  distcorr_options.add_argument('-topup_options', metavar='" TopupOptions"', help='Manually provide additional command-line options to the topup command (provide a string within quotation marks that contains at least one space, even if only passing a single command-line option to topup)')
+  distcorr_options.add_argument('-topup_files', metavar='prefix', help='Provide files generated by prior execution of the FSL "topup" command to be utilised by eddy')
   cmdline.flag_mutually_exclusive_options( [ 'topup_files', 'se_epi' ], False )
   cmdline.flag_mutually_exclusive_options( [ 'topup_files', 'align_seepi' ], False )
   cmdline.flag_mutually_exclusive_options( [ 'topup_files', 'topup_options' ], False )
   eddy_options = cmdline.add_argument_group('Options for affecting the operation of the FSL "eddy" command')
-  eddy_options.add_argument('-eddy_mask', metavar=('image'), help='Provide a processing mask to use for eddy, instead of having dwifslpreproc generate one internally using dwi2mask')
-  eddy_options.add_argument('-eddy_slspec', metavar=('file'), help='Provide a file containing slice groupings for eddy\'s slice-to-volume registration')
-  eddy_options.add_argument('-eddy_options', metavar=('" EddyOptions"'), help='Manually provide additional command-line options to the eddy command (provide a string within quotation marks that contains at least one space, even if only passing a single command-line option to eddy)')
+  eddy_options.add_argument('-eddy_mask', type=app.Parser.ImageIn(), metavar='image', help='Provide a processing mask to use for eddy, instead of having dwifslpreproc generate one internally using dwi2mask')
+  eddy_options.add_argument('-eddy_slspec', type=app.Parser.FileIn(), metavar='file', help='Provide a file containing slice groupings for eddy\'s slice-to-volume registration')
+  eddy_options.add_argument('-eddy_options', metavar='" EddyOptions"', help='Manually provide additional command-line options to the eddy command (provide a string within quotation marks that contains at least one space, even if only passing a single command-line option to eddy)')
   eddyqc_options = cmdline.add_argument_group('Options for utilising EddyQC')
-  eddyqc_options.add_argument('-eddyqc_text', metavar=('directory'), help='Copy the various text-based statistical outputs generated by eddy, and the output of eddy_qc (if installed), into an output directory')
-  eddyqc_options.add_argument('-eddyqc_all', metavar=('directory'), help='Copy ALL outputs generated by eddy (including images), and the output of eddy_qc (if installed), into an output directory')
+  eddyqc_options.add_argument('-eddyqc_text', type=app.Parser.DirectoryOut(), metavar='directory', help='Copy the various text-based statistical outputs generated by eddy, and the output of eddy_qc (if installed), into an output directory')
+  eddyqc_options.add_argument('-eddyqc_all', type=app.Parser.DirectoryOut(), metavar='directory', help='Copy ALL outputs generated by eddy (including images), and the output of eddy_qc (if installed), into an output directory')
   cmdline.flag_mutually_exclusive_options( [ 'eddyqc_text', 'eddyqc_all' ], False )
   app.add_dwgrad_export_options(cmdline)
   app.add_dwgrad_import_options(cmdline)

bin/dwigradcheck

@@ -29,8 +29,8 @@ def usage(cmdline): #pylint: disable=unused-variable
                           'More information on mask derivation from DWI data can be found at the following link: \n'
                           'https://mrtrix.readthedocs.io/en/' + _version.__tag__ + '/dwi_preprocessing/masking.html')
   cmdline.add_citation('Jeurissen, B.; Leemans, A.; Sijbers, J. Automated correction of improperly rotated diffusion gradient orientations in diffusion weighted MRI. Medical Image Analysis, 2014, 18(7), 953-962')
-  cmdline.add_argument('input', help='The input DWI series to be checked')
-  cmdline.add_argument('-mask', metavar='image', help='Provide a mask image within which to seed & constrain tracking')
+  cmdline.add_argument('input', type=app.Parser.ImageIn(), help='The input DWI series to be checked')
+  cmdline.add_argument('-mask', metavar='image', type=app.Parser.ImageIn(), help='Provide a mask image within which to seed & constrain tracking')
   cmdline.add_argument('-number', type=int, default=10000, help='Set the number of tracks to generate for each test')
 
   app.add_dwgrad_export_options(cmdline)

bin/dwishellmath

@@ -26,9 +26,9 @@ def usage(cmdline): #pylint: disable=unused-variable
   cmdline.add_description('The output of this command is a 4D image, where '
                           'each volume corresponds to a b-value shell (in order of increasing b-value), and '
                           'the intensities within each volume correspond to the chosen statistic having been computed from across the DWI volumes belonging to that b-value shell.')
-  cmdline.add_argument('input', help='The input diffusion MRI series')
+  cmdline.add_argument('input', type=app.Parser.ImageIn(), help='The input diffusion MRI series')
   cmdline.add_argument('operation', choices=SUPPORTED_OPS, help='The operation to be applied to each shell; this must be one of the following: ' + ', '.join(SUPPORTED_OPS))
-  cmdline.add_argument('output', help='The output image series')
+  cmdline.add_argument('output', type=app.Parser.ImageOut(), help='The output image series')
   cmdline.add_example_usage('To compute the mean diffusion-weighted signal in each b-value shell',
                             'dwishellmath dwi.mif mean shellmeans.mif')
   app.add_dwgrad_import_options(cmdline)
@@ -37,6 +37,8 @@ def usage(cmdline): #pylint: disable=unused-variable
 def execute(): #pylint: disable=unused-variable
   from mrtrix3 import MRtrixError #pylint: disable=no-name-in-module, import-outside-toplevel
   from mrtrix3 import app, image, path, run #pylint: disable=no-name-in-module, import-outside-toplevel
+  import sys
+
   # check inputs and outputs
   dwi_header = image.Header(path.from_user(app.ARGS.input, False))
   if len(dwi_header.size()) != 4:
@@ -63,6 +65,9 @@ def execute(): #pylint: disable=unused-variable
     # make a 4D image with one volume
     app.warn('Only one unique b-value present in DWI data; command mrmath with -axis 3 option may be preferable')
     run.command('mrconvert ' + files[0] + ' ' + path.from_user(app.ARGS.output) + ' -axes 0,1,2,-1', mrconvert_keyval=path.from_user(app.ARGS.input, False), force=app.FORCE_OVERWRITE)
+
+  if('mrtrix-tmp-' in app.ARGS.output):
+    sys.stdout.write(app.ARGS.output)
 
 
 # Execute the script

bin/labelsgmfix

@@ -30,15 +30,16 @@ import math, os
 
 
 def usage(cmdline): #pylint: disable=unused-variable
+  from mrtrix3 import app
   cmdline.set_author('Robert E. Smith (robert.smith@florey.edu.au)')
   cmdline.set_synopsis('In a FreeSurfer parcellation image, replace the sub-cortical grey matter structure delineations using FSL FIRST')
   cmdline.add_citation('Patenaude, B.; Smith, S. M.; Kennedy, D. N. & Jenkinson, M. A Bayesian model of shape and appearance for subcortical brain segmentation. NeuroImage, 2011, 56, 907-922', is_external=True)
   cmdline.add_citation('Smith, S. M.; Jenkinson, M.; Woolrich, M. W.; Beckmann, C. F.; Behrens, T. E.; Johansen-Berg, H.; Bannister, P. R.; De Luca, M.; Drobnjak, I.; Flitney, D. E.; Niazy, R. K.; Saunders, J.; Vickers, J.; Zhang, Y.; De Stefano, N.; Brady, J. M. & Matthews, P. M. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 2004, 23, S208-S219', is_external=True)
   cmdline.add_citation('Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. The effects of SIFT on the reproducibility and biological accuracy of the structural connectome. NeuroImage, 2015, 104, 253-265')
-  cmdline.add_argument('parc',   help='The input FreeSurfer parcellation image')
-  cmdline.add_argument('t1',     help='The T1 image to be provided to FIRST')
-  cmdline.add_argument('lut',    help='The lookup table file that the parcellated image is based on')
-  cmdline.add_argument('output', help='The output parcellation image')
+  cmdline.add_argument('parc', type=app.Parser.ImageIn(), help='The input FreeSurfer parcellation image')
+  cmdline.add_argument('t1', type=app.Parser.ImageIn(), help='The T1 image to be provided to FIRST')
+  cmdline.add_argument('lut', type=app.Parser.FileIn(), help='The lookup table file that the parcellated image is based on')
+  cmdline.add_argument('output', type=app.Parser.ImageOut(), help='The output parcellation image')
   cmdline.add_argument('-premasked', action='store_true', default=False, help='Indicate that brain masking has been applied to the T1 input image')
   cmdline.add_argument('-sgm_amyg_hipp', action='store_true', default=False, help='Consider the amygdalae and hippocampi as sub-cortical grey matter structures, and also replace their estimates with those from FIRST')
 

bin/mask2glass

@@ -16,6 +16,7 @@
 # For more details, see http://www.mrtrix.org/.
 
 def usage(cmdline): #pylint: disable=unused-variable
+  from mrtrix3 import app
   cmdline.set_author('Remika Mito (remika.mito@florey.edu.au) and Robert E. Smith (robert.smith@florey.edu.au)')
   cmdline.set_synopsis('Create a glass brain from mask input')
   cmdline.add_description('The output of this command is a glass brain image, which can be viewed '
@@ -24,8 +25,8 @@ def usage(cmdline): #pylint: disable=unused-variable
                           'also operate on a floating-point image. One way in which this can be exploited is to compute the mean '
                           'of all subject masks within template space, in which case this script will produce a smoother result '
                           'than if a binary template mask were to be used as input.')
-  cmdline.add_argument('input', help='The input mask image')
-  cmdline.add_argument('output', help='The output glass brain image')
+  cmdline.add_argument('input', type=app.Parser.ImageIn(), help='The input mask image')
+  cmdline.add_argument('output', type=app.Parser.ImageOut(), help='The output glass brain image')
   cmdline.add_argument('-dilate', type=int, default=2, help='Provide number of passes for dilation step; default = 2')
   cmdline.add_argument('-scale', type=float, default=2.0, help='Provide resolution upscaling value; default = 2.0')
   cmdline.add_argument('-smooth', type=float, default=1.0, help='Provide standard deviation of smoothing (in mm); default = 1.0')