Update Python code for recent changes on dev.

python/mrtrix3/commands/dwimotioncorrect.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 #   Copyright (c) 2017-2019 Daan Christiaens
 #
 #   MRtrix and this add-on module are distributed in the hope
@@ -17,7 +15,6 @@
 #            [email protected]
 #
 
-import mrtrix3
 from mrtrix3 import app, image, path, run, MRtrixError
 import json
 
@@ -150,7 +147,7 @@ def get_max_sh_degree(N, oversampling_factor=1.3):
         for l in range(0,10,2):
             if (l+3)*(l+4)/2 * oversampling_factor > N:
                 return l
- 
+
     lmax = [(b>10) * get_max_sh_degree(n) for b, n in zip(shells, shell_sizes)]
     if app.ARGS.lmax:
         lmax = [int(l) for l in app.ARGS.lmax.split(',')]
@@ -204,7 +201,7 @@ def get_max_sh_degree(N, oversampling_factor=1.3):
     nthr = ''
     if app.ARGS.nthreads:
         nthr = ' -nthreads ' + str(app.ARGS.nthreads)
-        
+
     # Set multiband factor
     mb = 1
     if app.ARGS.mb:
@@ -332,5 +329,4 @@ def fieldalignstep(k):
         run.command('cp sliceweights.txt ' + path.from_user(app.ARGS.export_weights, True))
 
 
-mrtrix3.execute()
 

python/mrtrix3/commands/motionfilter.py

@@ -1,7 +1,20 @@
-#!/usr/bin/env python
+#   Copyright (c) 2017-2019 Daan Christiaens
+#
+#   MRtrix and this add-on module are distributed in the hope
+#   that it will be useful, but WITHOUT ANY WARRANTY; without
+#   even the implied warranty of MERCHANTABILITY or FITNESS
+#   FOR A PARTICULAR PURPOSE.
+#
+#   MOTION CORRECTION FOR DWI VOLUME SERIES
+#
+#   This script performs volume-to-series and slice-to-series registration
+#   of diffusion-weighted images for motion correction in the brain.
+#
+#   Author:  Daan Christiaens
+#            King's College London
+#            [email protected]
+#
 
-import argparse
-import math
 import numpy as np
 from scipy.linalg import logm, expm
 from scipy.signal import medfilt
@@ -11,31 +24,37 @@ def getsliceorder(n, p=2, s=1):
     return np.array([j for k in range(0,p) for j in range((k*s)%p,n,p)], dtype=int)
 
 
-if __name__ == '__main__':
-    # arguments
-    parser = argparse.ArgumentParser(description='Filtering a series of rigid motion parameters.')
-    parser.add_argument('input', type=str, help='input motion file')
-    parser.add_argument('weights', type=str, help='input weight matrix')
-    parser.add_argument('output', type=str, help='output motion file')
-    #parser.add_argument('-mb', type=int, default=1, help='multiband factor')
-    parser.add_argument('-packs', type=int, default=2, help='no. slice packs')
-    parser.add_argument('-shift', type=int, default=1, help='slice shift')
-    parser.add_argument('-medfilt', type=int, default=1, help='median filtering kernel size (default = 1; disabled)')
-    parser.add_argument('-driftfilt', action='store_true', help='drift filter slice packs')
-    # mandatory MRtrix options (unused)
-    parser.add_argument('-nthreads', type=int, default=1, help='no. threads (unused)')
-    parser.add_argument('-info', help='(unused)')
-    parser.add_argument('-debug', help='(unused)')
-    parser.add_argument('-quiet', help='(unused)')
-    parser.add_argument('-force', help='(unused)')
-    args = parser.parse_args()
+def usage(cmdline): #pylint: disable=unused-variable
+  from mrtrix3 import app #pylint: disable=no-name-in-module, import-outside-toplevel
+  cmdline.set_author('Daan Christiaens ([email protected])')
+  cmdline.set_synopsis('Filtering a series of rigid motion parameters')
+  cmdline.add_description('This command applies a filter on a timeseries of rigid motion parameters.'
+                          ' This is used in dwimotioncorrect to correct severe registration errors.')
+  cmdline.add_argument('input',
+                       type=app.Parser.FileIn(),
+                       help='The input motion file')
+  cmdline.add_argument('weights',
+                       type=app.Parser.FileIn(),
+                       help='The input weight matrix')
+  cmdline.add_argument('output',
+                       type=app.Parser.FileOut(),
+                       help='The output motion file')
+  cmdline.add_argument('-packs', type=int, default=2, help='no. slice packs')
+  cmdline.add_argument('-shift', type=int, default=1, help='slice shift')
+  cmdline.add_argument('-medfilt', type=int, default=1, help='median filtering kernel size (default = 1; disabled)')
+  cmdline.add_argument('-driftfilt', action='store_true', help='drift filter slice packs')
+
+
+def execute(): #pylint: disable=unused-variable
+    from mrtrix3 import MRtrixError #pylint: disable=no-name-in-module, import-outside-toplevel
+    from mrtrix3 import app, image, run #pylint: disable=no-name-in-module, import-outside-toplevel
     # read inputs
-    M = np.loadtxt(args.input)
-    W = np.clip(np.loadtxt(args.weights), 1e-6, None)
+    M = np.loadtxt(app.ARGS.input)
+    W = np.clip(np.loadtxt(app.ARGS.weights), 1e-6, None)
     # set up slice order
     nv = W.shape[1]
     ne = M.shape[0]//nv
-    sliceorder = getsliceorder(ne, args.packs, args.shift)
+    sliceorder = getsliceorder(ne, app.ARGS.packs, app.ARGS.shift)
     isliceorder = np.argsort(sliceorder)
     # reorder
     M1 = np.reshape(M.reshape((nv,ne,6))[:,sliceorder,:], (-1,6))
@@ -47,11 +66,10 @@ def getsliceorder(n, p=2, s=1):
     M2 = np.linalg.solve(A, W1 * M1)
     # median filtering
     if ne > 1:
-        M2 = medfilt(M2, (args.medfilt, 1))
-    if args.driftfilt:
+        M2 = medfilt(M2, (app.ARGS.medfilt, 1))
+    if app.ARGS.driftfilt:
         M2 = M2.reshape((nv,ne,6)) - np.median(M2.reshape((nv,ne,6)), 0)
     # reorder output
     M3 = np.reshape(M2.reshape((nv,ne,6))[:,isliceorder,:], (-1,6))
-    np.savetxt(args.output, M3, fmt='%.6f')
-
+    np.savetxt(app.ARGS.output, M3, fmt='%.6f')
 

python/mrtrix3/commands/motionstats.py

@@ -1,7 +1,15 @@
-#!/usr/bin/env python
+#   Copyright (c) 2017-2019 Daan Christiaens
+#
+#   MRtrix and this add-on module are distributed in the hope
+#   that it will be useful, but WITHOUT ANY WARRANTY; without
+#   even the implied warranty of MERCHANTABILITY or FITNESS
+#   FOR A PARTICULAR PURPOSE.
+#
+#   Author:  Daan Christiaens
+#            King's College London
+#            [email protected]
+#
 
-import argparse
-import math
 import numpy as np
 from scipy.linalg import logm, expm
 import matplotlib.pyplot as plt
@@ -46,32 +54,35 @@ def tr2euler(T):
     return np.array([T[0,3], T[1,3], T[2,3], yaw, pitch, roll])
 
 
+def usage(cmdline): #pylint: disable=unused-variable
+    from mrtrix3 import app #pylint: disable=no-name-in-module, import-outside-toplevel
+    cmdline.set_author('Daan Christiaens ([email protected])')
+    cmdline.set_synopsis('Calculate motion and outlier statistics')
+    cmdline.add_description('This command calculates statistics of the subject translation and rotation'
+                            ' and of the detected slice outliers.')
+    cmdline.add_argument('input',
+                         type=app.Parser.FileIn(),
+                         help='The input motion file')
+    cmdline.add_argument('weights',
+                         type=app.Parser.FileIn(),
+                         help='The input weight matrix')
+    cmdline.add_argument('-packs', type=int, default=2, help='no. slice packs')
+    cmdline.add_argument('-shift', type=int, default=1, help='slice shift')
+    cmdline.add_argument('-plot', action='store_true', help='plot motion trajectory')
+    cmdline.add_argument('-grad', type=app.Parser.FileIn(), help='dMRI gradient table')
+    cmdline.add_argument('-dispersion', type=app.Parser.FileIn(), help='output gradient dispersion to file')
 
-if __name__ == '__main__':
-    # arguments
-    parser = argparse.ArgumentParser(description='Calculate motion and outlier statistics.')
-    parser.add_argument('input', type=str, help='input motion file')
-    parser.add_argument('weights', type=str, help='input weight matrix')
-    #parser.add_argument('-mb', type=int, default=1, help='multiband factor')
-    parser.add_argument('-packs', type=int, default=2, help='no. slice packs')
-    parser.add_argument('-shift', type=int, default=1, help='slice shift')
-    parser.add_argument('-plot', action='store_true', help='plot motion trajectory')
-    parser.add_argument('-grad', type=str, help='dMRI gradient table')
-    parser.add_argument('-dispersion', type=str, help='output gradient dispersion to file')
-    # mandatory MRtrix options (unused)
-    parser.add_argument('-nthreads', type=int, default=1, help='no. threads (unused)')
-    parser.add_argument('-info', action='store_true', help='(unused)')
-    parser.add_argument('-debug', action='store_true', help='(unused)')
-    parser.add_argument('-quiet', action='store_true', help='(unused)')
-    parser.add_argument('-force', action='store_true', help='(unused)')
-    args = parser.parse_args()
+
+def execute(): #pylint: disable=unused-variable
+    from mrtrix3 import MRtrixError #pylint: disable=no-name-in-module, import-outside-toplevel
+    from mrtrix3 import app, image #pylint: disable=no-name-in-module, import-outside-toplevel
     # read inputs
-    M0 = np.loadtxt(args.input)
-    W = np.loadtxt(args.weights)
+    M0 = np.loadtxt(app.ARGS.input)
+    W = np.loadtxt(app.ARGS.weights)
     # set up slice order
     nv = W.shape[1]
     ne = M0.shape[0]//nv
-    sliceorder = getsliceorder(ne, args.packs, args.shift)
+    sliceorder = getsliceorder(ne, app.ARGS.packs, app.ARGS.shift)
     isliceorder = np.argsort(sliceorder)
     # reorder
     M = np.reshape(M0.reshape((nv,ne,6))[:,sliceorder,:], (-1,6))
@@ -84,22 +95,22 @@ def tr2euler(T):
     # print stats
     print('{:f} {:f} {:f}'.format(mtra, mrot, orratio))
     # plot trajectory
-    if args.plot:
+    if app.ARGS.plot:
         T = np.array([tr2euler(lie2tr(m)) for m in M])
         ax1 = plt.subplot(2,1,1); plt.plot(T[:,:3]); plt.ylabel('translation'); plt.legend(['x', 'y', 'z']);
         ax2 = plt.subplot(2,1,2, sharex=ax1); plt.plot(T[:,3:]); plt.ylabel('rotation'); plt.legend(['yaw', 'pitch', 'roll']);
         plt.xlim(0, nv*ne); plt.xlabel('time'); plt.tight_layout();
         plt.show();
     # intra-volume gradient scatter
-    if args.dispersion:
-        if args.grad:
-            grad = np.loadtxt(args.grad)
+    if app.ARGS.dispersion:
+        if app.ARGS.grad:
+            grad = np.loadtxt(app.ARGS.grad)
             bvec = grad[:,:3] / np.linalg.norm(grad[:,:3], axis=1)[:,np.newaxis]
             r = np.array([[np.dot(lie2tr(m)[:3,:3], v) for m in mvol] for mvol, v in zip(M.reshape((nv,ne,6)), bvec)])
             rm = np.sum(r, axis=1); rm /= np.linalg.norm(rm, axis=1)[:,np.newaxis]
             rd = np.einsum('vzi,vi->vz', r, rm)
             dispersion = np.degrees(2*np.arccos(np.sqrt(np.mean(rd**2, axis=1))))
-            np.savetxt(args.dispersion, dispersion[np.newaxis,:], fmt='%.4f')
+            np.savetxt(app.ARGS.dispersion, dispersion[np.newaxis,:], fmt='%.4f')
         else:
-            print('error: gradient table not provided.')
+            raise MRtrixError('No diffusion gradient table provided')