Initial import

.gitattributes

+*.nii.gz filter=lfs diff=lfs merge=lfs -text

EddyS2VTest/CompareMovementOverTime.py

+#!/usr/bin/env fslpython
+# CompareMovementOverTime.py - script for comparing two .eddy_movement_over_time files.
+#
+"""
+Usage:
+CompareMovementOverTime.py 'test .eddy_movement_over_time' 'ref .eddy_movement_over_time' max_allowed_max_trans_diff max_allowed_99percentile_trans_diff max_allowed_mean_trans_diff max_allowed_max_rot_diff max_allowed_99percentile_rot_diff max_allowed_mean_rot_diff
+or 
+CompareMovementOverTime.py 'test .eddy_movement_over_time' 'ref .eddy_movement_over_time' max_allowed_max_trans_diff max_allowed_99percentile_trans_diff max_allowed_mean_trans_diff max_allowed_max_rot_diff max_allowed_99percentile_rot_diff max_allowed_mean_rot_diff number_of_slices_in_data first_slice_to_check last_slice_to_check
+"""
+
+from __future__ import print_function # I have no words...
+
+import sys
+import CompareTextOutputDef as ct
+
+if __name__ == '__main__':
+    try:
+        if len(sys.argv) == 1:
+            print(__doc__)
+            exit(1)
+
+        if len(sys.argv) == 10:
+            are_the_same = ct.MovementOverTimeAreSame(sys.argv[1],sys.argv[2],float(sys.argv[3]),float(sys.argv[4]),float(sys.argv[5]),float(sys.argv[6]),float(sys.argv[7]),float(sys.argv[8]),int(sys.argv[9]))
+        elif len(sys.argv) == 13:
+            are_the_same = ct.MovementOverTimeAreSame(sys.argv[1],sys.argv[2],float(sys.argv[3]),float(sys.argv[4]),float(sys.argv[5]),float(sys.argv[6]),float(sys.argv[7]),float(sys.argv[8]),int(sys.argv[9]),int(sys.argv[10]),int(sys.argv[11]),int(sys.argv[12]))
+        else:
+            are_the_same = False
+            print('CompareMovementOverTime: Invalid number of input arguments: {}'.format(len(sys.argv)-1),file=sys.stderr)
+
+        
+        if are_the_same == True:
+            sys.exit(0)
+        else:
+            sys.exit(1)
+    except Exception as e:
+        print('CompareMovementOverTime: Unknown error: {}'.format(e.args[0]),file=sys.stderr)
+        sys.exit(1)
+
+    print('CompareMovementOverTime: Unknown error2',file=sys.stderr)
+    sys.exit(1)
+

EddyS2VTest/CompareMovementOverTime.py~

+#!/usr/bin/env fslpython
+# CompareMovementOverTime.py - script for comparing two .eddy_movement_over_time files.
+#
+"""
+Usage:
+CompareMovementOverTime.py 'test .eddy_movement_over_time' 'ref .eddy_movement_over_time' max_allowed_max_trans_diff max_allowed_99percentile_trans_diff max_allowed_mean_trans_diff max_allowed_max_rot_diff max_allowed_99percentile_rot_diff max_allowed_mean_rot_diff
+or 
+CompareMovementOverTime.py 'test .eddy_movement_over_time' 'ref .eddy_movement_over_time' max_allowed_max_trans_diff max_allowed_99percentile_trans_diff max_allowed_mean_trans_diff max_allowed_max_rot_diff max_allowed_99percentile_rot_diff max_allowed_mean_rot_diff number_of_slices_in_data first_slice_to_check last_slice_to_check
+"""
+
+from __future__ import print_function # I have no words...
+
+import sys
+import CompareTextOutputDef as ct
+
+if __name__ == '__main__':
+    try:
+        if len(sys.argv) == 1:
+            print(__doc__)
+            exit(1)
+
+        if len(sys.argv) == 10:
+            are_the_same = ct.MovementOverTimeAreSame(sys.argv[1],sys.argv[2],float(sys.argv[3]),float(sys.argv[4]),float(sys.argv[5]),float(sys.argv[6]),float(sys.argv[7]),float(sys.argv[8]),int(sys.argv[9]))
+        elif len(sys.argv) == 13:
+            are_the_same = ct.MovementOverTimeAreSame(sys.argv[1],sys.argv[2],float(sys.argv[3]),float(sys.argv[4]),float(sys.argv[5]),float(sys.argv[6]),float(sys.argv[7]),float(sys.argv[8]),int(sys.argv[9]),int(sys.argv[10]),int(sys.argv[11]),int(sys.argv[12]))
+            print('I am here and are_the_same = {}'.format(are_the_same))
+        else:
+            are_the_same = False
+            print('CompareMovementOverTime: Invalid number of input arguments: {}'.format(len(sys.argv)),file=sys.stderr)
+
+        
+        print('I am here and now are_the_same = {}'.format(are_the_same))
+        if are_the_same == True:
+            print('I am about to exit with code 0')
+            sys.exit(0)
+        else:
+            sys.exit(1)
+    except:
+        # raise
+        print('CompareMovementOverTime: Unknown error1',file=sys.stderr)
+        sys.exit(1)
+
+    print('CompareMovementOverTime: Unknown error2',file=sys.stderr)
+    sys.exit(1)
+

EddyS2VTest/CompareOutlierNStdevMaps.py

+#!/usr/bin/env fslpython
+# CompareOutlierNStdevMaps.py - script for comparing two .eddy_outlier_n_stdev_map files.
+#
+"""
+Usage:
+CompareOutlierNStdevMaps.py 'test .eddy_outlier_n_stdev_map' 'ref .eddy_outlier_n_stdev_map' max_allowed_max_relative_z_score_diff_for_z>1 max_allowed_mean_relative_z_score_diff_for_z>1 max_allowed_max_relative_z_score_diff_for_z>2 max_allowed_mean_relative_z_score_diff_for_z>2
+or 
+CompareOutlierNStdevMaps.py 'test .eddy_outlier_n_stdev_map' 'ref .eddy_outlier_n_stdev_map' max_allowed_max_relative_z_score_diff_for_z>1 max_allowed_mean_relative_z_score_diff_for_z>1 max_allowed_max_relative_z_score_diff_for_z>2 max_allowed_mean_relative_z_score_diff_for_z>2 number_of_slices_in_data first_slice_to_check last_slice_to_check
+"""
+
+from __future__ import print_function # I have no words...
+
+import sys
+import CompareTextOutputDef as ct
+
+if __name__ == '__main__':
+    try:
+        if len(sys.argv) == 1:
+            print(__doc__)
+            are_the_same = false
+        if len(sys.argv) == 7:
+            are_the_same = ct.OutlierNStdevMapsAreTheSame(sys.argv[1],sys.argv[2],float(sys.argv[3]),float(sys.argv[4]),float(sys.argv[5]),float(sys.argv[6]))
+        elif len(sys.argv) == 10:
+            are_the_same = ct.OutlierNStdevMapsAreTheSame(sys.argv[1],sys.argv[2],float(sys.argv[3]),float(sys.argv[4]),float(sys.argv[5]),float(sys.argv[6]),int(sys.argv[7]),int(sys.argv[8]),int(sys.argv[9]))
+        else:
+            print('CompareOutlierNStdevMaps: Invalid number of input arguments: {}'.format(len(sys.argv)-1),file=sys.stderr)
+        if are_the_same == True:
+            exit(0)
+        else:
+            exit(1)
+    except Exception as e:
+        print('CompareOutlierNStdevMaps: Unknown error: {}'.format(e.args[0]),file=sys.stderr)
+        exit(1)
+
+    print('CompareOutlierNStdevMaps: Unknown error',file=sys.stderr)
+    exit(1)
+

EddyS2VTest/CompareOutlierNStdevMaps.py~

+#!/usr/bin/env fslpython
+# CompareOutlierNStdevMaps.py - script for comparing two .eddy_outlier_n_stdev_map files.
+#
+"""
+Usage:
+CompareOutlierNStdevMaps.py 'test .eddy_outlier_n_stdev_map' 'ref .eddy_outlier_n_stdev_map' max_allowed_max_relative_z_score_diff_for_z>1 max_allowed_mean_relative_z_score_diff_for_z>1 max_allowed_max_relative_z_score_diff_for_z>2 max_allowed_mean_relative_z_score_diff_for_z>2
+or 
+CompareOutlierNStdevMaps.py 'test .eddy_outlier_n_stdev_map' 'ref .eddy_outlier_n_stdev_map' max_allowed_max_relative_z_score_diff_for_z>1 max_allowed_mean_relative_z_score_diff_for_z>1 max_allowed_max_relative_z_score_diff_for_z>2 max_allowed_mean_relative_z_score_diff_for_z>2 number_of_slices_in_data first_slice_to_check last_slice_to_check
+"""
+
+from __future__ import print_function # I have no words...
+
+import sys
+import CompareTextOutputDef as ct
+
+if __name__ == '__main__':
+    try:
+        if len(sys.argv) == 1:
+            print(__doc__)
+            are_the_same = false
+        if len(sys.argv) == 7:
+            are_the_same = ct.OutlierNStdevMapsAreTheSame(sys.argv[1],sys.argv[2],float(sys.argv[3]),float(sys.argv[4]),float(sys.argv[5]),float(sys.argv[6]))
+        elif len(sys.argv) == 10:
+            are_the_same = ct.OutlierNStdevMapsAreTheSame(sys.argv[1],sys.argv[2],float(sys.argv[3]),float(sys.argv[4]),float(sys.argv[5]),float(sys.argv[6]),int(sys.argv[7]),int(sys.argv[8]),int(sys.argv[9]))
+        else:
+            print('CompareOutlierNStdevMaps: Invalid number of input arguments: {}'.format(len(sys.argv)),file=sys.stderr)
+        if are_the_same == True:
+            exit(0)
+        else:
+            exit(1)
+    except:
+        print('CompareOutlierNStdevMaps: Unknown error',file=sys.stderr)
+        exit(1)
+
+    print('CompareOutlierNStdevMaps: Unknown error',file=sys.stderr)
+    exit(1)
+

EddyS2VTest/CompareTextOutputDef.py

+#!/usr/bin/env python
+# CompareTextOutputDef.py - contains defs for comparing textual output from eddy
+# It has code for comparing two .eddy_movement_over_time files and for comparing
+# two .eddy_outlier_n_stdev_map files.
+#
+
+from __future__ import print_function # I have no words...
+
+import            collections
+import            datetime
+import            tempfile
+import            logging
+import            shutil
+import            fnmatch
+import            re
+import            sys
+import            os
+import os.path as op
+import numpy   as np
+
+def MovementOverTimeAreSame(testfname, reffname, maxtrans, trans99, meantrans, maxrot, rot99, meanrot, skip, *args):
+    """Compares two .eddy_movement_over_time files and returns true or false.
+    Pass or fail depends on observed differences compared to limits specified by
+    inputs maxtrans, trans99, meantrans, maxrot, rot99 and meanrot. Skip is 0 or 1 if 
+    we are to skip comparison for x-trans (0) or y-trans (1). If not, skip should be -1.
+    USE: MovementOverTimeAreSame(testfname, reffname, maxtrans, trans99, meantrans, maxrot, rot99, meanrot, skip)
+    or
+    MovementOverTimeAreSame(testfname, reffname, maxtrans, trans99, meantrans, maxrot, rot99, meanrot, skip, nsl, fsl, lsl)
+    """
+
+    if (skip < -1) or (skip > 1):
+        print('MovementOverTimeAreSame: Invalid skip value',file=sys.stderr)
+        raise ValueError('MovementOverTimeAreSame: Invalid skip value')
+
+    if len(args) != 0 and len(args) != 3:
+        print('MovementOverTimeAreSame: Invalid number of optional arguments',file=sys.stderr)
+        raise RuntimeError('MovementOverTimeAreSame: Invalid number of optional arguments')
+
+    if len(args) == 3:
+        nsl = args[0]
+        fsl = args[1]
+        lsl = args[2]
+        if fsl < 0 or lsl > (nsl-1):
+            print('MovementOverTimeAreSame: Invalid fsl or lsl',file=sys.stderr)
+            raise ValueError('MovementOverTimeAreSame: Invalid fsl or lsl')
+
+    try:
+        test_data = np.genfromtxt(testfname)
+        ref_data = np.genfromtxt(reffname)
+    except Exception as e:
+        print('MovementOverTimeAreSame: File read error: {}'.format(e.args[0]),file=sys.stderr)
+        raise e
+
+    if test_data.shape != ref_data.shape or test_data.shape[1] != 6 or test_data.shape[0] % nsl != 0:
+        print('MovementOverTimeAreSame: Shape mismatch between files {} and {}'.format(testfname,reffname),file=sys.stderr)
+        raise ValueError('MovementOverTimeAreSame: Shape mismatch between files {} and {}'.format(testfname,reffname))
+
+    # Remove end slices if nsl, fsl and lsl have been set
+    if len(args) == 3:
+        try:
+            if test_data.shape[0] % nsl:
+                raise ValueError('')
+            for p in range(0,6):
+                tmp = test_data[:,p]
+                tmp = np.reshape(tmp,(nsl,test_data.shape[0]//nsl),'F') 
+                tmp = tmp[fsl:lsl+1,:]
+                if p == 0:
+                    tmp_test_data = np.reshape(tmp,(tmp.size,1),'F')
+                else:
+                    tmp_test_data = np.concatenate((tmp_test_data,np.reshape(tmp,(tmp.size,1),'F')),axis=1)
+                tmp = ref_data[:,p]
+                tmp = np.reshape(tmp,(nsl,test_data.shape[0]//nsl),'F') 
+                tmp = tmp[fsl:lsl+1,:]
+                if p == 0:
+                    tmp_ref_data = np.reshape(tmp,(tmp.size,1),'F')
+                else:
+                    tmp_ref_data = np.concatenate((tmp_ref_data,np.reshape(tmp,(tmp.size,1),'F')),axis=1)
+        except Exception as e:
+            print('MovementOverTimeAreSame: Input nsl={}, fsl={} or lsl={} not suited for files {} and {}'.format(nsl,fsl,lsl,testfname,reffname),file=sys.stderr)
+            raise ValueError('MovementOverTimeAreSame: Input nsl={}, fsl={} or lsl={} not suited for files {} and {}'.format(nsl,fsl,lsl,testfname,reffname))
+
+
+
+    test_data = tmp_test_data
+    ref_data = tmp_ref_data
+
+
+    diff = test_data - ref_data
+    absdiff = np.absolute(diff)
+    if skip == 0:
+        atdiff = absdiff[:,[1, 2]]
+    elif skip == 1:
+        atdiff = absdiff[:,[0, 2]]
+    elif skip == -1:
+        atdiff = absdiff[:,[0, 1, 2]]
+    
+    ardiff = 180.0 * absdiff[:,[3, 4, 5]] / 3.141593    
+    
+    omaxtrans = np.amax(atdiff)                                    # Max translation
+    omaxrot = np.amax(ardiff)                                      # Max rotation
+    omeantrans = np.max(np.mean(atdiff,0))                         # Mean translation along worst direction
+    omeanrot = np.max(np.mean(ardiff,0))                           # Mean rotation around worst axis
+    otrans99 = np.max(np.sort(atdiff,0)[int(0.99*len(atdiff)),:])  # 99th percentile along worst direction
+    orot99 = np.max(np.sort(ardiff,0)[int(0.99*len(atdiff)),:])    # 99th percentile around worst axis
+
+    print('MovementOverTimeAreSame: maxtrans = {}, maxrot = {}'.format(maxtrans,maxrot),file=sys.stdout)
+    print('MovementOverTimeAreSame: omaxtrans = {}, omaxrot = {}'.format(omaxtrans,omaxrot),file=sys.stdout)
+    print('MovementOverTimeAreSame: meantrans = {}, meanrot = {}'.format(meantrans,meanrot),file=sys.stdout)
+    print('MovementOverTimeAreSame: omeantrans = {}, omeanrot = {}'.format(omeantrans,omeanrot),file=sys.stdout)
+    print('MovementOverTimeAreSame: trans99 = {}, rot99 = {}'.format(trans99,rot99),file=sys.stdout)
+    print('MovementOverTimeAreSame: otrans99 = {}, orot99 = {}'.format(otrans99,orot99),file=sys.stdout)
+
+    rval = True
+    if (omaxtrans > maxtrans) or (omaxrot > maxrot) or (otrans99 > trans99) or (orot99 > rot99) or (omeantrans > meantrans) or (omeanrot > meanrot):
+        rval = False
+    
+    return rval
+
+def OutlierNStdevMapsAreTheSame(testfname, reffname, maxdiff1, meandiff1, maxdiff2, meandiff2, *args):
+    """Compares two .eddy_outlier_n_stdev_map files and returns true or false.
+    Pass or fail depends on observed differences compared to limits specified by
+    inputs maxdiff1, meandiff1, maxdiff2 and meandiff2.
+    USE: OutlierNStdevMapsAreTheSame(testfname, reffname, maxdiff1, meandiff1, maxdiff2, meandiff2)
+    or
+    OutlierNStdevMapsAreTheSame(testfname, reffname, maxdiff1, meandiff1, maxdiff2, meandiff2, nsl, fsl, lsl)
+    """
+
+    if len(args) != 0 and len(args) != 3:
+        print('OutlierNStdevMapsAreTheSame: Invalid number of optional arguments',file=sys.stderr)
+        raise ValueError('OutlierNStdevMapsAreTheSame: Invalid number of optional arguments')
+    if len(args) == 3:
+        nsl = args[0]
+        fsl = args[1]
+        lsl = args[2]
+        if fsl < 0 or lsl > (nsl-1):
+            print('OutlierNStdevMapsAreTheSame: Invalid fsl or lsl',file=sys.stderr)
+            raise ValueError('OutlierNStdevMapsAreTheSame: Invalid fsl or lsl')
+
+    try:
+        test_data = np.genfromtxt(testfname,skip_header=1)
+        ref_data = np.genfromtxt(reffname,skip_header=1)
+    except Exception as e:
+        print('OutlierNStdevMapsAreTheSame: File read error: {}'.format(e.args[0]),file=sys.stderr)
+        raise e
+
+    if test_data.shape != ref_data.shape:
+        print('OutlierNStdevMapsAreTheSame: Shape mismatch between files {} and {}'.format(testfname,reffname),file=sys.stderr)
+        raise ValueError('OutlierNStdevMapsAreTheSame: Shape mismatch between files {} and {}'.format(testfname,reffname))
+
+    if len(args) == 3:
+        if nsl != ref_data.shape[1]:
+            print('OutlierNStdevMapsAreTheSame: Shape mismatch between the files {} and {} and nsl={}'.format(testfname,reffname,nsl),file=sys.stderr)
+            raise ValueError('OutlierNStdevMapsAreTheSame: Shape mismatch between the files {} and {} and nsl={}'.format(testfname,reffname,nsl))
+        ref_data = ref_data[:,fsl:lsl+1]
+        test_data = test_data[:,fsl:lsl+1]
+
+    try:
+        # Find vol-slice tuples that are non-zero in both runs
+        nztest = test_data != 0
+        nzref = ref_data != 0
+        if float(np.sum(nzref)-np.sum(nztest)) / np.sum(nzref) > 0.01: # Ensure ~ equal no. of non-zero
+            print('OutlierNStdevMapsAreTheSame: Large mismatch in number of slices considered',file=sys.stdout)
+            return False
+
+        mask = np.multiply(nztest.astype('int'),nzref.astype('int'))
+        indx = np.where(mask > 0)
+        test_data = test_data[indx]
+        ref_data = ref_data[indx]
+
+        # Calculate difference-ratio for all non-zero tuples
+        radiff = np.divide(np.absolute(test_data - ref_data),np.absolute(ref_data))
+
+        # Check for max and mean diff-ratio for voxels with z > 1
+        indx2 = np.where(ref_data > 1.0)
+        omaxdiff1 = np.max(radiff[indx2])
+        omeandiff1 = np.mean(radiff[indx2])
+
+        # Check for max and mean diff-ratio for voxels with z > 2    
+        indx2 = np.where(ref_data > 2.0)
+        omaxdiff2 = np.max(radiff[indx2])
+        omeandiff2 = np.mean(radiff[indx2])
+
+        print('OutlierNStdevMapsAreTheSame: maxdiff1 = {}, omaxdiff1 = {}'.format(maxdiff1,omaxdiff1),file=sys.stdout)
+        print('OutlierNStdevMapsAreTheSame: meandiff1 = {}, omeandiff1 = {}'.format(meandiff1,omeandiff1),file=sys.stdout)
+        print('OutlierNStdevMapsAreTheSame: maxdiff2 = {}, omaxdiff2 = {}'.format(maxdiff2,omaxdiff2),file=sys.stdout)
+        print('OutlierNStdevMapsAreTheSame: meandiff2 = {}, omeandiff2 = {}'.format(meandiff2,omeandiff2),file=sys.stdout)
+
+    except Exception as e:
+        print('OutlierNStdevMapsAreTheSame: Unknown error: {}'.format(e.args[0]),file=sys.stderr)
+        raise e
+
+
+    rval = True
+    if (omaxdiff1 > maxdiff1) or (omeandiff1 > meandiff1) or (omaxdiff2 > maxdiff2) or (omeandiff2 > meandiff2):
+        rval = False
+
+    return rval

EddyS2VTest/CompareTextOutputDef.py~

+#!/usr/bin/env python
+# CompareTextOutputDef.py - contains defs for comparing textual output from eddy
+# It has code for comparing two .eddy_movement_over_time files and for comparing
+# two .eddy_outlier_n_stdev_map files.
+#
+
+from __future__ import print_function # I have no words...
+
+import            collections
+import            datetime
+import            tempfile
+import            logging
+import            shutil
+import            fnmatch
+import            re
+import            sys
+import            os
+import os.path as op
+import numpy   as np
+
+def MovementOverTimeAreSame(testfname, reffname, maxtrans, trans99, meantrans, maxrot, rot99, meanrot, skip, *args):
+    """Compares two .eddy_movement_over_time files and returns true or false.
+    Pass or fail depends on observed differences compared to limits specified by
+    inputs maxtrans, trans99, meantrans, maxrot, rot99 and meanrot. Skip is 0 or 1 if 
+    we are to skip comparison for x-trans (0) or y-trans (1). If not, skip should be -1.
+    USE: MovementOverTimeAreSame(testfname, reffname, maxtrans, trans99, meantrans, maxrot, rot99, meanrot, skip)
+    or
+    MovementOverTimeAreSame(testfname, reffname, maxtrans, trans99, meantrans, maxrot, rot99, meanrot, skip, nsl, fsl, lsl)
+    """
+
+    if (skip < -1) or (skip > 1):
+        print('MovementOverTimeAreSame: Invalid skip value',file=sys.stderr)
+        return False
+
+    if len(args) != 0 and len(args) != 3:
+        print('MovementOverTimeAreSame: Invalid number of optional arguments',file=sys.stderr)
+        return False
+
+    if len(args) == 3:
+        nsl = args[0]
+        fsl = args[1]
+        lsl = args[2]
+        if fsl < 0 or lsl > (nsl-1):
+            print('MovementOverTimeAreSame: Invalid fsl or lsl',file=sys.stderr)
+            return False
+
+    try:
+        test_data = np.genfromtxt(testfname)
+        ref_data = np.genfromtxt(reffname)
+    except:
+        print('MovementOverTimeAreSame: Unable to read file {} or {}'.format(testfname,reffname),file=sys.stderr)
+        return False
+
+    if test_data.shape != ref_data.shape or test_data.shape[1] != 6 or test_data.shape[0] % nsl != 0:
+        print('MovementOverTimeAreSame: Shape mismatch between files {} and {}'.format(testfname,reffname),file=sys.stderr)
+        return False
+
+    # Remove end slices if nsl, fsl and lsl have been set
+    if len(args) == 3:
+        try:
+            for p in range(0,6):
+                tmp = test_data[:,p]
+                tmp = np.reshape(tmp,(nsl,test_data.shape[0]/nsl),'F') 
+                tmp = tmp[fsl:lsl+1,:]
+                if p == 0:
+                    tmp_test_data = np.reshape(tmp,(tmp.size,1),'F')
+                else:
+                    tmp_test_data = np.concatenate((tmp_test_data,np.reshape(tmp,(tmp.size,1),'F')),axis=1)
+                tmp = ref_data[:,p]
+                tmp = np.reshape(tmp,(nsl,test_data.shape[0]/nsl),'F') 
+                tmp = tmp[fsl:lsl+1,:]
+                if p == 0:
+                    tmp_ref_data = np.reshape(tmp,(tmp.size,1),'F')
+                else:
+                    tmp_ref_data = np.concatenate((tmp_ref_data,np.reshape(tmp,(tmp.size,1),'F')),axis=1)
+        except:
+            print('MovementOverTimeAreSame: Input nsl, fsl or lsl not suited for files {} and {}'.format(testfname,reffname),file=sys.stderr)
+            return False
+
+
+
+    test_data = tmp_test_data
+    ref_data = tmp_ref_data
+
+
+    diff = test_data - ref_data
+    absdiff = np.absolute(diff)
+    if skip == 0:
+        atdiff = absdiff[:,[1, 2]]
+    elif skip == 1:
+        atdiff = absdiff[:,[0, 2]]
+    elif skip == -1:
+        atdiff = absdiff[:,[0, 1, 2]]
+    
+    ardiff = 180.0 * absdiff[:,[3, 4, 5]] / 3.141593    
+    
+    omaxtrans = np.amax(atdiff)                                    # Max translation
+    omaxrot = np.amax(ardiff)                                      # Max rotation
+    omeantrans = np.max(np.mean(atdiff,0))                         # Mean translation along worst direction
+    omeanrot = np.max(np.mean(ardiff,0))                           # Mean rotation around worst axis
+    otrans99 = np.max(np.sort(atdiff,0)[int(0.99*len(atdiff)),:])  # 99th percentile along worst direction
+    orot99 = np.max(np.sort(ardiff,0)[int(0.99*len(atdiff)),:])    # 99th percentile around worst axis
+
+    print('MovementOverTimeAreSame: maxtrans = {}, maxrot = {}'.format(maxtrans,maxrot),file=sys.stdout)
+    print('MovementOverTimeAreSame: omaxtrans = {}, omaxrot = {}'.format(omaxtrans,omaxrot),file=sys.stdout)
+    print('MovementOverTimeAreSame: meantrans = {}, meanrot = {}'.format(meantrans,meanrot),file=sys.stdout)
+    print('MovementOverTimeAreSame: omeantrans = {}, omeanrot = {}'.format(omeantrans,omeanrot),file=sys.stdout)
+    print('MovementOverTimeAreSame: trans99 = {}, rot99 = {}'.format(trans99,rot99),file=sys.stdout)
+    print('MovementOverTimeAreSame: otrans99 = {}, orot99 = {}'.format(otrans99,orot99),file=sys.stdout)
+
+    rval = True
+    if (omaxtrans > maxtrans) or (omaxrot > maxrot) or (otrans99 > trans99) or (orot99 > rot99) or (omeantrans > meantrans) or (omeanrot > meanrot):
+        rval = False
+    
+    print('I am about to return')
+    return rval
+
+def OutlierNStdevMapsAreTheSame(testfname, reffname, maxdiff1, meandiff1, maxdiff2, meandiff2, *args):
+    """Compares two .eddy_outlier_n_stdev_map files and returns true or false.
+    Pass or fail depends on observed differences compared to limits specified by
+    inputs maxdiff1, meandiff1, maxdiff2 and meandiff2.
+    USE: OutlierNStdevMapsAreTheSame(testfname, reffname, maxdiff1, meandiff1, maxdiff2, meandiff2)
+    or
+    OutlierNStdevMapsAreTheSame(testfname, reffname, maxdiff1, meandiff1, maxdiff2, meandiff2, nsl, fsl, lsl)
+    """
+
+    if len(args) != 0 and len(args) != 3:
+        print('OutlierNStdevMapsAreTheSame: Invalid number of optional arguments',file=sys.stderr)
+        return False
+    if len(args) == 3:
+        nsl = args[0]
+        fsl = args[1]
+        lsl = args[2]
+        if fsl < 0 or lsl > (nsl-1):
+            print('OutlierNStdevMapsAreTheSame: Invalid fsl or lsl',file=sys.stderr)
+            return False
+
+    try:
+        test_data = np.genfromtxt(testfname,skip_header=1)
+        ref_data = np.genfromtxt(reffname,skip_header=1)
+    except:
+        print('OutlierNStdevMapsAreTheSame: Unable to read file {} or {}'.format(testfname,reffname),file=sys.stderr)
+        return False
+
+    if test_data.shape != ref_data.shape:
+        print('OutlierNStdevMapsAreTheSame: Shape mismatch between files {} and {}'.format(testfname,reffname),file=sys.stderr)
+        return False
+
+    if len(args) == 3:
+        if nsl != ref_data.shape[1]:
+            print('OutlierNStdevMapsAreTheSame: Shape mismatch between the files {} and {} and nsl'.format(testfname,reffname),file=sys.stderr)
+            return False
+        ref_data = ref_data[:,fsl:lsl+1]
+        test_data = test_data[:,fsl:lsl+1]
+
+    try:
+        # Find vol-slice tuples that are non-zero in both runs
+        nztest = test_data != 0
+        nzref = ref_data != 0
+        if float(np.sum(nzref)-np.sum(nztest)) / np.sum(nzref) > 0.01: # Ensure ~ equal no. of non-zero
+            print('OutlierNStdevMapsAreTheSame: Large mismatch in number of slices considered',file=sys.stdout)
+            return False
+
+        mask = np.multiply(nztest.astype('int'),nzref.astype('int'))
+        indx = np.where(mask > 0)
+        test_data = test_data[indx]
+        ref_data = ref_data[indx]
+
+        # Calculate difference-ratio for all non-zero tuples
+        radiff = np.divide(np.absolute(test_data - ref_data),np.absolute(ref_data))
+
+        # Check for max and mean diff-ratio for voxels with z > 1
+        indx2 = np.where(ref_data > 1.0)
+        omaxdiff1 = np.max(radiff[indx2])
+        omeandiff1 = np.mean(radiff[indx2])
+
+        # Check for max and mean diff-ratio for voxels with z > 2    
+        indx2 = np.where(ref_data > 2.0)
+        omaxdiff2 = np.max(radiff[indx2])
+        omeandiff2 = np.mean(radiff[indx2])
+
+        print('OutlierNStdevMapsAreTheSame: maxdiff1 = {}, omaxdiff1 = {}'.format(maxdiff1,omaxdiff1),file=sys.stdout)
+        print('OutlierNStdevMapsAreTheSame: meandiff1 = {}, omeandiff1 = {}'.format(meandiff1,omeandiff1),file=sys.stdout)
+        print('OutlierNStdevMapsAreTheSame: maxdiff2 = {}, omaxdiff2 = {}'.format(maxdiff2,omaxdiff2),file=sys.stdout)
+        print('OutlierNStdevMapsAreTheSame: meandiff2 = {}, omeandiff2 = {}'.format(meandiff2,omeandiff2),file=sys.stdout)
+
+    except:
+        print('OutlierNStdevMapsAreTheSame: Unknown error',file=sys.stderr)
+        return False
+
+
+    rval = True
+    if (omaxdiff1 > maxdiff1) or (omeandiff1 > meandiff1) or (omaxdiff2 > maxdiff2) or (omeandiff2 > meandiff2):
+        rval = False
+
+    return rval

EddyS2VTest/feedsInputs

+EddyS2VTestData/eddyData

EddyS2VTest/feedsInputs~

+EddyTestData/eddyData

EddyS2VTest/feedsRun

+#! /bin/sh
+#
+# This script runs eddy on data with intra-volume movement,
+# followed by some tests on the output.
+# It uses simulated data supplied by Mark
+# Graham, UCL, which allows us to have a ground
+# truth. The data is a subset of that used
+# for the s2v paper.
+# At the time of writing this (May, 2017) the openmp version
+# is not able to do slice-to-vol realignment. Hence only
+# the cuda version is tested. The script should be updated
+# if/when there is an openmp implementation of slice-to-vol.
+#
+
+scriptdir=`dirname $0`
+odir=$1
+indir=$2
+#
+# Inputs 1--2 are the ones neccessary for feeds to work
+# Additional inputs are optional and intended for testing
+# outside of the feeds context.
+#
+# Input 3 is alternative location of executable
+#
+if [ "$#" -gt 2 ]; then
+    exedir=$3
+   echo "Directory for eddy executables set to ${exedir}"
+else
+   exedir="${FSLDIR}/bin"
+fi 
+
+if [ ! -x "${exedir}/eddy_cuda" ]; then
+   echo "Executable ${exedir}/eddy_cuda does not exist"
+   exit 1
+fi
+#if [ ! -x "${exedir}/eddy_openmp" ]; then
+#   echo "Executable ${exedir}/eddy_openmp does not exist"
+#   exit 1
+#fi
+ 
+if [ ! -d "$odir" ]; then
+   echo "Output directory ${odir} does not exist" 
+   exit 1;
+fi
+if [ ! -d "$indir" ]; then
+   echo "Input directory ${odir} does not exist" 
+   exit 1;
+fi
+
+# Define some constants
+
+# These are for the comparison of output images divided on b=0, b=700 and b=2000
+max_mean_ima_diff="1.8 0.6 0.5"
+max_max_ima_diff="2.0 0.7 0.6"
+
+# Launch both GPU and CPU versions
+ 
+cuda_jid=`fsl_sub -q cuda.q ${exedir}/eddy_cuda --imain=${indir}/EddyS2VTestData/eddyData/testData --mask=${indir}/EddyS2VTestData/eddyData/testMask --bvals=${indir}/EddyS2VTestData/eddyData/testBvals --bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs --index=${indir}/EddyS2VTestData/eddyData/testIndex --acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams --repol --ol_type=slice --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/eddyCudaOutput --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose`
+
+# omp_jid=`fsl_sub -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyS2VTestData/eddyData/testData --mask=${indir}/EddyS2VTestData/eddyData/testMask --bvals=${indir}/EddyS2VTestData/eddyData/testBvals --bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs --index=${indir}/EddyS2VTestData/eddyData/testIndex --acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams --repol --ol_type=slice --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/eddyCudaOutput --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose`
+
+# Wait until they have both finished
+
+while [ : ]; do
+   tmp=`qstat -j ${cuda_jid} | wc`
+   tmp=`echo $tmp | awk '{print $1}'`
+#   if [ $tmp -eq 0 ]; then
+#      tmp=`qstat -j ${omp_jid} | wc`
+#      tmp=`echo $tmp | awk '{print $1}'`
+      if [ $tmp -eq 0 ]; then
+      	 break
+      fi
+#   fi
+   sleep 5m
+done
+
+# Check that eddy output exists
+
+if [ ! -f ${odir}/eddyCudaOutput.nii* ]; then
+   exit 1
+fi
+#if [ ! -f ${odir}/eddyOmpOutput.nii* ]; then
+#   exit 1
+#fi
+
+# Check the results against ground truth
+
+# First compare output images
+
+mmidiff=""
+maxidiff=""
+# for oname in eddyCudaOutput eddyOmpOutput; do
+for oname in eddyCudaOutput; do
+   fslmaths ${indir}/EddyS2VTestData/eddyData/GroundTruth/ground_truth -sub ${odir}/${oname} -abs ${odir}/${oname}_diff_tmp
+   # Divide into different shells
+   for bv in 0 700 2000; do
+       select_dwi_vols ${odir}/${oname}_diff_tmp ${indir}/EddyS2VTestData/eddyData/testBvals ${odir}/${oname}_diff_tmp_b${bv} ${bv}
+   done
+   imrm ${odir}/${oname}_diff_tmp
+   # Remove top and bottom slides with no data in the eddy output
+   for bv in 0 700 2000; do
+       fslroi ${odir}/${oname}_diff_tmp_b${bv} ${odir}/${oname}_diff_tmp_b${bv} 2 68 4 80 6 44
+   done
+   fslroi ${indir}/EddyS2VTestData/eddyData/testMask ${odir}/tmp_mask 2 68 4 80 6 44
+
+   for bv in 0 700 2000; do
+       mdiff=$(fslstats -t ${odir}/${oname}_diff_tmp_b${bv} -k ${odir}/tmp_mask -m)		     
+       imrm ${odir}/${oname}_diff_tmp_b${bv}
+       echo $mdiff > ${odir}/${oname}.ima_mean_diff_b${bv}.txt
+       echo "feedsRun: Mean difference per volume is: ${mdiff} for shell b=${bv}"
+       mmidiff="${mmidiff} $(echo $mdiff | awk '{sum=0; for (i=1; i<=NF; i++) { sum+= $i } print sum/NF}')"
+       maxidiff="${maxidiff} $(tr ' ' '\n' <<<$mdiff | sort -r | head -n1)"
+   done
+done
+echo "Avrage mean abolute differences for shells 0, 700 and 2000 are: ${mmidiff}"
+echo "Acceptable average mean absolute differences for shells 0, 700 and 2000 are: ${max_mean_ima_diff}"
+echo "Maximum mean absolute differences for shells 0, 700 and 2000 are: ${maxidiff}"
+echo "Acceptable maximum mean absolute differences for shells 0, 700 and 2000 are: ${max_max_ima_diff}"
+
+# Next decide on fail or pass
+
+# Mean diff for b0
+fail=$(echo "$(echo $mmidiff | awk '{print $1}') > $(echo $max_mean_ima_diff | awk '{print $1}')" | bc)
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed because mean diff for b=0 too large"
+   exit 1;
+fi
+# Mean diff for b700
+fail=$(echo "$(echo $mmidiff | awk '{print $2}') > $(echo $max_mean_ima_diff | awk '{print $2}')" | bc)
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed because mean diff for b=700 too large"
+   exit 1;
+fi
+# Mean diff for b2000
+fail=$(echo "$(echo $mmidiff | awk '{print $3}') > $(echo $max_mean_ima_diff | awk '{print $3}')" | bc)
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed because mean diff for b=2000 too large"
+   exit 1;
+fi
+
+# Max diff for b0
+fail=$(echo "$(echo $maxidiff | awk '{print $1}') > $(echo $max_max_ima_diff | awk '{print $1}')" | bc)
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed because max diff for b=0 too large"
+   exit 1;
+fi
+# Max diff for b700
+fail=$(echo "$(echo $maxidiff | awk '{print $2}') > $(echo $max_max_ima_diff | awk '{print $2}')" | bc)
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed because max diff for b=700 too large"
+   exit 1;
+fi
+# Max diff for b2000
+fail=$(echo "$(echo $maxidiff | awk '{print $2}') > $(echo $max_max_ima_diff | awk '{print $2}')" | bc)
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed because max diff for b=2000 too large"
+   exit 1;
+fi
+
+#
+# Next do checks on output text files
+#
+# First .eddy_movement_over_time
+#
+echo "Now running CompareMovementOverTime.py"
+${scriptdir}/CompareMovementOverTime.py ${odir}/${oname}.eddy_movement_over_time ${indir}/EddyS2VTestData/eddyData/MovementTruth/ground_truth.eddy_movement_over_time 1.0 1.0 0.2 3.0 1.5 0.3 1 55 7 46
+fail=$?
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed in CompareMovementOverTime.py"
+   exit 1;
+fi
+
+#
+# Next .eddy_outlier_n_stdev_map 
+#
+echo "Now running CompareOutlierNStdevMaps.py"
+${scriptdir}/CompareOutlierNStdevMaps.py ${odir}/${oname}.eddy_outlier_n_stdev_map ${indir}/EddyS2VTestData/eddyData/NStdevMapRef/ref.eddy_outlier_n_stdev_map 0.2 0.03 0.05 0.02 55 7 46
+fail=$?
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed in CompareOutlierNStdevMaps.py"
+   exit 1;
+fi
+
+exit 0

EddyS2VTest/feedsRun~

+#! /bin/sh
+#
+# This script runs eddy on data with intra-volume movement,
+# followed by some tests on the output.
+# It uses simulated data supplied by Mark
+# Graham, UCL, which allows us to have a ground
+# truth. The data is a subset of that used
+# for the s2v paper.
+# At the time of writing this (May, 2017) the openmp version
+# is not able to do slice-to-vol realignment. Hence only
+# the cuda version is tested. The script should be updated
+# if/when there is an openmp implementation of slice-to-vol.
+#
+
+scriptdir=`dirname $0`
+odir=$1
+indir=$2
+#
+# Inputs 1--2 are the ones neccessary for feeds to work
+# Additional inputs are optional and intended for testing
+# outside of the feeds context.
+#
+# Input 3 is alternative location of executable
+#
+if [ "$#" -gt 2 ]; then
+    exedir=$3
+   echo "Directory for eddy executables set to ${exedir}"
+else
+   exedir="${FSLDIR}/bin"
+fi 
+
+if [ ! -x "${exedir}/eddy_cuda" ]; then
+   echo "Executable ${exedir}/eddy_cuda does not exist"
+   exit 1
+fi
+#if [ ! -x "${exedir}/eddy_openmp" ]; then
+#   echo "Executable ${exedir}/eddy_openmp does not exist"
+#   exit 1
+#fi
+ 
+if [ ! -d "$odir" ]; then
+   echo "Output directory ${odir} does not exist" 
+   exit 1;
+fi
+if [ ! -d "$indir" ]; then
+   echo "Input directory ${odir} does not exist" 
+   exit 1;
+fi
+
+# Define some constants
+
+# These are for the comparison of output images divided on b=0, b=700 and b=2000
+max_mean_ima_diff="1.8 0.6 0.5"
+max_max_ima_diff="2.0 0.7 0.6"
+
+# Launch both GPU and CPU versions
+
+if false; then
+ 
+cuda_jid=`fsl_sub -q cuda.q ${exedir}/eddy_cuda --imain=${indir}/EddyS2VTestData/eddyData/testData --mask=${indir}/EddyS2VTestData/eddyData/testMask --bvals=${indir}/EddyS2VTestData/eddyData/testBvals --bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs --index=${indir}/EddyS2VTestData/eddyData/testIndex --acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams --repol --ol_type=slice --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/eddyCudaOutput --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose`
+
+# omp_jid=`fsl_sub -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyS2VTestData/eddyData/testData --mask=${indir}/EddyS2VTestData/eddyData/testMask --bvals=${indir}/EddyS2VTestData/eddyData/testBvals --bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs --index=${indir}/EddyS2VTestData/eddyData/testIndex --acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams --repol --ol_type=slice --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/eddyCudaOutput --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose`
+
+# Wait until they have both finished
+
+while [ : ]; do
+   tmp=`qstat -j ${cuda_jid} | wc`
+   tmp=`echo $tmp | awk '{print $1}'`
+#   if [ $tmp -eq 0 ]; then
+#      tmp=`qstat -j ${omp_jid} | wc`
+#      tmp=`echo $tmp | awk '{print $1}'`
+      if [ $tmp -eq 0 ]; then
+      	 break
+      fi
+#   fi
+   sleep 5m
+done
+
+# Check that eddy output exists
+
+if [ ! -f ${odir}/eddyCudaOutput.nii* ]; then
+   exit 1
+fi
+#if [ ! -f ${odir}/eddyOmpOutput.nii* ]; then
+#   exit 1
+#fi
+
+# Check the results against ground truth
+
+# First compare output images
+
+mmidiff=""
+maxidiff=""
+# for oname in eddyCudaOutput eddyOmpOutput; do
+for oname in eddyCudaOutput; do
+   fslmaths ${indir}/EddyS2VTestData/eddyData/GroundTruth/ground_truth -sub ${odir}/${oname} -abs ${odir}/${oname}_diff_tmp
+   # Divide into different shells
+   for bv in 0 700 2000; do
+       select_dwi_vols ${odir}/${oname}_diff_tmp ${indir}/EddyS2VTestData/eddyData/testBvals ${odir}/${oname}_diff_tmp_b${bv} ${bv}
+   done
+   imrm ${odir}/${oname}_diff_tmp
+   # Remove top and bottom slides with no data in the eddy output
+   for bv in 0 700 2000; do
+       fslroi ${odir}/${oname}_diff_tmp_b${bv} ${odir}/${oname}_diff_tmp_b${bv} 2 68 4 80 6 44
+   done
+   fslroi ${indir}/EddyS2VTestData/eddyData/testMask ${odir}/tmp_mask 2 68 4 80 6 44
+
+   for bv in 0 700 2000; do
+       mdiff=$(fslstats -t ${odir}/${oname}_diff_tmp_b${bv} -k ${odir}/tmp_mask -m)		     
+       imrm ${odir}/${oname}_diff_tmp_b${bv}
+       echo $mdiff > ${odir}/${oname}.ima_mean_diff_b${bv}.txt
+       echo "feedsRun: Mean difference per volume is: ${mdiff} for shell b=${bv}"
+       mmidiff="${mmidiff} $(echo $mdiff | awk '{sum=0; for (i=1; i<=NF; i++) { sum+= $i } print sum/NF}')"
+       maxidiff="${maxidiff} $(tr ' ' '\n' <<<$mdiff | sort -r | head -n1)"
+   done
+done
+echo "Avrage mean abolute differences for shells 0, 700 and 2000 are: ${mmidiff}"
+echo "Acceptable average mean absolute differences for shells 0, 700 and 2000 are: ${max_mean_ima_diff}"
+echo "Maximum mean absolute differences for shells 0, 700 and 2000 are: ${maxidiff}"
+echo "Acceptable maximum mean absolute differences for shells 0, 700 and 2000 are: ${max_max_ima_diff}"
+
+# Next decide on fail or pass
+
+# Mean diff for b0
+fail=$(echo "$(echo $mmidiff | awk '{print $1}') > $(echo $max_mean_ima_diff | awk '{print $1}')" | bc)
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed because mean diff for b=0 too large"
+   exit 1;
+fi
+# Mean diff for b700
+fail=$(echo "$(echo $mmidiff | awk '{print $2}') > $(echo $max_mean_ima_diff | awk '{print $2}')" | bc)
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed because mean diff for b=700 too large"
+   exit 1;
+fi
+# Mean diff for b2000
+fail=$(echo "$(echo $mmidiff | awk '{print $3}') > $(echo $max_mean_ima_diff | awk '{print $3}')" | bc)
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed because mean diff for b=2000 too large"
+   exit 1;
+fi
+
+# Max diff for b0
+fail=$(echo "$(echo $maxidiff | awk '{print $1}') > $(echo $max_max_ima_diff | awk '{print $1}')" | bc)
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed because max diff for b=0 too large"
+   exit 1;
+fi
+# Max diff for b700
+fail=$(echo "$(echo $maxidiff | awk '{print $2}') > $(echo $max_max_ima_diff | awk '{print $2}')" | bc)
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed because max diff for b=700 too large"
+   exit 1;
+fi
+# Max diff for b2000
+fail=$(echo "$(echo $maxidiff | awk '{print $2}') > $(echo $max_max_ima_diff | awk '{print $2}')" | bc)
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed because max diff for b=2000 too large"
+   exit 1;
+fi
+
+fi # End if false
+
+oname="eddyCudaOutput"
+
+#
+# Next do checks on output text files
+#
+# First .eddy_movement_over_time
+#
+echo "Now running CompareMovementOverTime.py"
+${scriptdir}/CompareMovementOverTime.py ${odir}/${oname}.eddy_movement_over_time ${indir}/EddyS2VTestData/eddyData/MovementTruth/ground_truth.eddy_movement_over_time 1.0 1.0 0.2 3.0 1.5 0.3 1 55 7 46
+fail=$?
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed in CompareMovementOverTime.py"
+   exit 1;
+fi
+
+#
+# Next .eddy_outlier_n_stdev_map 
+#
+echo "Now running CompareOutlierNStdevMaps.py"
+${scriptdir}/CompareOutlierNStdevMaps.py ${odir}/${oname}.eddy_outlier_n_stdev_map ${indir}/EddyS2VTestData/eddyData/NStdevMapRef/ref.eddy_outlier_n_stdev_map 0.2 0.03 0.05 0.02 55 7 46
+fail=$?
+if [ $fail -gt 0 ]; then
+   echo "feedsRun: Test failed in CompareOutlierNStdevMaps.py"
+   exit 1;
+fi
+
+exit 0

EddyTest/eddy_cuda.e2286236

+
+Part of FSL (build 508)
+eddy 
+Copyright(c) 2015, University of Oxford (Jesper Andersson)
+
+Usage: 
+eddy --monsoon
+
+Compulsory arguments (You MUST set one or more of):
+	--imain	File containing all the images to estimate distortions for
+	--mask	Mask to indicate brain
+	--index	File containing indices for all volumes in --imain into --acqp and --topup
+	--acqp	File containing acquisition parameters
+	--bvecs	File containing the b-vectors for all volumes in --imain
+	--bvals	File containing the b-values for all volumes in --imain
+	--out	Basename for output
+
+Optional arguments (You may optionally specify one or more of):
+	--mb	Multi-band factor
+	--mb_offs	Multi-band offset (-1 if bottom slice removed, 1 if top slice removed)
+	--topup	Base name for output files from topup
+	--field	Name of file with susceptibility field (in Hz)
+	--field_mat	Name of rigid body transform for susceptibility field
+	--flm	First level EC model (linear/quadratic/cubic, default quadratic)
+	--slm	Second level EC model (none/linear/quadratic, default none)
+	--fwhm	FWHM for conditioning filter when estimating the parameters (default 0)
+	--niter	Number of iterations (default 5)
+	--fep	Fill empty planes in x- or y-directions
+	--interp	Interpolation model for estimation step (spline/trilinear, default spline)
+	--resamp	Final resampling method (jac/lsr, default jac)
+	--nvoxhp	# of voxels used to estimate the hyperparameters (default 1000)
+	--initrand	Resets rand for when selecting voxels (default false)
+	--ff	Fudge factor for hyperparameter error variance (default 10.0)
+	--repol	Detect and replace outlier slices
+	--ol_nstd	Number of std off to qualify as outlier (default 4)
+	--ol_nvox	Min # of voxels in a slice for inclusion in outlier detection (default 250)
+	--ol_type	Type of outliers, slicewise (sw), groupwise (gw) or both (both). (default sw)
+	--ol_pos	Consider both positive and negative outliers if set (default false)
+	--ol_sqr	Consider outliers among sums-of-squared differences if set (default false)
+	--dont_sep_offs_move	Do NOT attempt to separate field offset from subject movement (default false)
+	--dont_peas	Do NOT perform a post-eddy alignment of shells (default false)
+	--data_is_shelled	Assume, don't check, that data is shelled (default false)
+	-v,--verbose	switch on diagnostic messages
+	-h,--help	display this message
+
+
+
+--with_outliers: Option doesn't exist!

EddyTest/eddy_cuda.o2284102

+Reading images
+Performing volume-to-volume registration
+Running Register
+Entering EddyGpuUtils::LoadPredictionMaker
+
+...................Allocated GPU # 0...................
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 0, Total mss = 32.3879
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 1, Total mss = 69.4732
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 2, Total mss = 52.6548
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 3, Total mss = 52.3811
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 4, Total mss = 52.2441
+Running sm.Setb0Reference
+Running sm.PolateB0MovPar
+Running Register
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Checking for outliers
+Calculating parameter updates
+Iter: 0, Total mss = 0.794029
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Checking for outliers
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 1, Total mss = 16.7945
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Checking for outliers
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 2, Total mss = 16.3233
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Checking for outliers
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 3, Total mss = 16.3347
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Checking for outliers
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 4, Total mss = 16.1455
+Running sm.SetDWIReference
+Aligning shells (running PostEddyAlignShells)
+Performing final outlier check
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Checking for outliers
+Running sm.WriteOutlierFreeData
+Running sm.WriteParameterFile
+Running sm.WriteRegisteredImages
+Running sm.WriteRotatedBVecs
+Running sm.WriteMovementRMS
+Running sm.WriteDisplacementFields

EddyTest/eddy_cuda.o2286247

+Reading images
+Performing volume-to-volume registration
+Running Register
+Entering EddyGpuUtils::LoadPredictionMaker
+
+...................Allocated GPU # 0...................
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 0, Total mss = 32.3879
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 1, Total mss = 69.473
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 2, Total mss = 52.6673
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 3, Total mss = 52.3908
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 4, Total mss = 52.2527
+Running sm.Setb0Reference
+Running sm.PolateB0MovPar
+Running Register
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Checking for outliers
+Calculating parameter updates
+Iter: 0, Total mss = 0.776861
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Checking for outliers
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 1, Total mss = 16.6888
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Checking for outliers
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 2, Total mss = 16.3153
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Checking for outliers
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 3, Total mss = 16.2089
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Checking for outliers
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Calculating parameter updates
+Iter: 4, Total mss = 16.2899
+Running sm.SetDWIReference
+Aligning shells (running PostEddyAlignShells)
+Performing final outlier check
+Entering EddyGpuUtils::LoadPredictionMaker
+Loading prediction maker
+Evaluating prediction maker model
+Checking for outliers
+Running sm.WriteOutlierFreeData
+Running sm.WriteParameterFile
+Running sm.WriteRegisteredImages
+Running sm.WriteRegisteredImages
+Running sm.RecycleOutliers
+Running sm.WriteRotatedBVecs
+Running sm.WriteMovementRMS
+Running sm.WriteDisplacementFields