/usr/share/pyshared/nipype/interfaces/io.py is in python-nipype 0.5.3-2wheezy2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
""" Set of interfaces that allow interaction with data. Currently
available interfaces are:
DataSource: Generic nifti to named Nifti interface
DataSink: Generic named output from interfaces to data store
XNATSource: preliminary interface to XNAT
To come :
XNATSink
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
>>> os.chdir(datadir)
"""
import glob
import os
import shutil
import re
import tempfile
from warnings import warn
import sqlite3
try:
import pyxnat
except:
pass
from nipype.interfaces.base import (TraitedSpec, traits, File, Directory,
BaseInterface, InputMultiPath, isdefined,
OutputMultiPath, DynamicTraitedSpec,
Undefined, BaseInterfaceInputSpec)
from nipype.utils.filemanip import (copyfile, list_to_filename,
filename_to_list)
from .. import logging
iflogger = logging.getLogger('interface')
def copytree(src, dst):
"""Recursively copy a directory tree using
nipype.utils.filemanip.copyfile()
This is not a thread-safe routine. However, in the case of creating new
directories, it checks to see if a particular directory has already been
created by another process.
"""
names = os.listdir(src)
try:
os.makedirs(dst)
except OSError, why:
if 'File exists' in why:
pass
else:
raise why
errors = []
for name in names:
srcname = os.path.join(src, name)
dstname = os.path.join(dst, name)
try:
if os.path.isdir(srcname):
copytree(srcname, dstname)
else:
copyfile(srcname, dstname, True, hashmethod='content')
except (IOError, os.error), why:
errors.append((srcname, dstname, str(why)))
# catch the Error from the recursive copytree so that we can
# continue with other files
except Exception, err:
errors.extend(err.args[0])
if errors:
raise Exception, errors
def add_traits(base, names, trait_type=None):
""" Add traits to a traited class.
All traits are set to Undefined by default
"""
if trait_type is None:
trait_type = traits.Any
undefined_traits = {}
for key in names:
base.add_trait(key, trait_type)
undefined_traits[key] = Undefined
base.trait_set(trait_change_notify=False, **undefined_traits)
# access each trait
for key in names:
_ = getattr(base, key)
return base
class IOBase(BaseInterface):
def _run_interface(self,runtime):
return runtime
def _list_outputs(self):
raise NotImplementedError
def _outputs(self):
return self._add_output_traits(super(IOBase, self)._outputs())
def _add_output_traits(self, base):
return base
class DataSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
base_directory = Directory(
desc='Path to the base directory for storing data.')
container = traits.Str(desc = 'Folder within base directory in which to store output')
parameterization = traits.Bool(True, usedefault=True,
desc='store output in parametrized structure')
strip_dir = Directory(desc='path to strip out of filename')
substitutions = InputMultiPath(traits.Tuple(traits.Str,traits.Str),
desc=('List of 2-tuples reflecting string '
'to substitute and string to replace '
'it with'))
regexp_substitutions = InputMultiPath(traits.Tuple(traits.Str,traits.Str),
desc=('List of 2-tuples reflecting a pair '
'of a Python regexp pattern and a '
'replacement string. Invoked after '
'string `substitutions`'))
_outputs = traits.Dict(traits.Str, value={}, usedefault=True)
remove_dest_dir = traits.Bool(False, usedefault=True,
desc='remove dest directory when copying dirs')
def __setattr__(self, key, value):
if key not in self.copyable_trait_names():
if not isdefined(value):
super(DataSinkInputSpec, self).__setattr__(key, value)
self._outputs[key] = value
else:
if key in self._outputs:
self._outputs[key] = value
super(DataSinkInputSpec, self).__setattr__(key, value)
class DataSink(IOBase):
""" Generic datasink module to store structured outputs
Primarily for use within a workflow. This interface allows arbitrary
creation of input attributes. The names of these attributes define the
directory structure to create for storage of the files or directories.
The attributes take the following form:
string[[.[@]]string[[.[@]]string]] ...
where parts between [] are optional.
An attribute such as contrasts.@con will create a 'contrasts' directory
to store the results linked to the attribute. If the @ is left out, such
as in 'contrasts.con', a subdirectory 'con' will be created under
'contrasts'.
the general form of the output is::
'base_directory/container/parameterization/destloc/filename'
destloc = string[[.[@]]string[[.[@]]string]] and
filename comesfrom the input to the connect statement.
.. warning::
This is not a thread-safe node because it can write to a common
shared location. It will not complain when it overwrites a file.
.. note::
If both substitutions and regexp_substitutions are used, then
substitutions are applied first followed by regexp_substitutions.
This interface **cannot** be used in a MapNode as the inputs are
defined only when the connect statement is executed.
Examples
--------
>>> ds = DataSink()
>>> ds.inputs.base_directory = 'results_dir'
>>> ds.inputs.container = 'subject'
>>> ds.inputs.structural = 'structural.nii'
>>> setattr(ds.inputs, 'contrasts.@con', ['cont1.nii', 'cont2.nii'])
>>> setattr(ds.inputs, 'contrasts.alt', ['cont1a.nii', 'cont2a.nii'])
>>> ds.run() # doctest: +SKIP
To use DataSink in a MapNode, its inputs have to be defined at the
time the interface is created.
>>> ds = DataSink(infields=['contasts.@con'])
>>> ds.inputs.base_directory = 'results_dir'
>>> ds.inputs.container = 'subject'
>>> ds.inputs.structural = 'structural.nii'
>>> setattr(ds.inputs, 'contrasts.@con', ['cont1.nii', 'cont2.nii'])
>>> setattr(ds.inputs, 'contrasts.alt', ['cont1a.nii', 'cont2a.nii'])
>>> ds.run() # doctest: +SKIP
"""
input_spec = DataSinkInputSpec
def __init__(self, infields=None, **kwargs):
"""
Parameters
----------
infields : list of str
Indicates the input fields to be dynamically created
"""
super(DataSink, self).__init__(**kwargs)
undefined_traits = {}
# used for mandatory inputs check
self._infields = infields
if infields:
for key in infields:
self.inputs.add_trait(key, traits.Any)
self.inputs._outputs[key] = Undefined
undefined_traits[key] = Undefined
self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
def _get_dst(self, src):
path, fname = os.path.split(src)
if self.inputs.parameterization:
dst = path
if isdefined(self.inputs.strip_dir):
dst = dst.replace(self.inputs.strip_dir, '')
folders = [folder for folder in dst.split(os.path.sep) if
folder.startswith('_')]
dst = os.path.sep.join(folders)
if fname:
dst = os.path.join(dst, fname)
else:
if fname:
dst = fname
else:
dst = path.split(os.path.sep)[-1]
if dst[0] == os.path.sep:
dst = dst[1:]
return dst
def _substitute(self, pathstr):
pathstr_ = pathstr
if isdefined(self.inputs.substitutions):
for key, val in self.inputs.substitutions:
oldpathstr = pathstr
pathstr = pathstr.replace(key, val)
if pathstr != oldpathstr:
iflogger.debug('sub.str: %s -> %s using %r -> %r'
% (oldpathstr, pathstr, key, val))
if isdefined(self.inputs.regexp_substitutions):
for key, val in self.inputs.regexp_substitutions:
oldpathstr = pathstr
pathstr, _ = re.subn(key, val, pathstr)
if pathstr != oldpathstr:
iflogger.debug('sub.regexp: %s -> %s using %r -> %r'
% (oldpathstr, pathstr, key, val))
if pathstr_ != pathstr:
iflogger.info('sub: %s -> %s' % (pathstr_, pathstr))
return pathstr
def _list_outputs(self):
"""Execute this module.
"""
outdir = self.inputs.base_directory
if not isdefined(outdir):
outdir = '.'
outdir = os.path.abspath(outdir)
if isdefined(self.inputs.container):
outdir = os.path.join(outdir, self.inputs.container)
if not os.path.exists(outdir):
try:
os.makedirs(outdir)
except OSError, inst:
if 'File exists' in inst:
pass
else:
raise(inst)
for key, files in self.inputs._outputs.items():
if not isdefined(files):
continue
iflogger.debug("key: %s files: %s"%(key, str(files)))
files = filename_to_list(files)
tempoutdir = outdir
for d in key.split('.'):
if d[0] == '@':
continue
tempoutdir = os.path.join(tempoutdir,d)
# flattening list
if isinstance(files, list):
if isinstance(files[0], list):
files = [item for sublist in files for item in sublist]
for src in filename_to_list(files):
src = os.path.abspath(src)
if os.path.isfile(src):
dst = self._get_dst(src)
dst = os.path.join(tempoutdir, dst)
dst = self._substitute(dst)
path,_ = os.path.split(dst)
if not os.path.exists(path):
try:
os.makedirs(path)
except OSError, inst:
if 'File exists' in inst:
pass
else:
raise(inst)
iflogger.debug("copyfile: %s %s"%(src, dst))
copyfile(src, dst, copy=True, hashmethod='content')
elif os.path.isdir(src):
dst = self._get_dst(os.path.join(src,''))
dst = os.path.join(tempoutdir, dst)
dst = self._substitute(dst)
path,_ = os.path.split(dst)
if not os.path.exists(path):
try:
os.makedirs(path)
except OSError, inst:
if 'File exists' in inst:
pass
else:
raise(inst)
if os.path.exists(dst) and self.inputs.remove_dest_dir:
iflogger.debug("removing: %s"%dst)
shutil.rmtree(dst)
iflogger.debug("copydir: %s %s"%(src, dst))
copytree(src, dst)
return None
class DataGrabberInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec): #InterfaceInputSpec):
base_directory = Directory(exists=True,
desc='Path to the base directory consisting of subject data.')
raise_on_empty = traits.Bool(True, usedefault=True,
desc='Generate exception if list is empty for a given field')
sort_filelist = traits.Bool(False, usedefault=True,
desc='Sort the filelist that matches the template')
template = traits.Str(mandatory=True,
desc='Layout used to get files. relative to base directory if defined')
template_args = traits.Dict(key_trait=traits.Str,
value_trait= traits.List(traits.List),
desc='Information to plug into template')
class DataGrabber(IOBase):
""" Generic datagrabber module that wraps around glob in an
intelligent way for neuroimaging tasks to grab files
.. attention::
Doesn't support directories currently
Examples
--------
>>> from nipype.interfaces.io import DataGrabber
Pick all files from current directory
>>> dg = DataGrabber()
>>> dg.inputs.template = '*'
Pick file foo/foo.nii from current directory
>>> dg.inputs.template = '%s/%s.dcm'
>>> dg.inputs.template_args['outfiles']=[['dicomdir','123456-1-1.dcm']]
Same thing but with dynamically created fields
>>> dg = DataGrabber(infields=['arg1','arg2'])
>>> dg.inputs.template = '%s/%s.nii'
>>> dg.inputs.arg1 = 'foo'
>>> dg.inputs.arg2 = 'foo'
however this latter form can be used with iterables and iterfield in a
pipeline.
Dynamically created, user-defined input and output fields
>>> dg = DataGrabber(infields=['sid'], outfields=['func','struct','ref'])
>>> dg.inputs.base_directory = '.'
>>> dg.inputs.template = '%s/%s.nii'
>>> dg.inputs.template_args['func'] = [['sid',['f3','f5']]]
>>> dg.inputs.template_args['struct'] = [['sid',['struct']]]
>>> dg.inputs.template_args['ref'] = [['sid','ref']]
>>> dg.inputs.sid = 's1'
Change the template only for output field struct. The rest use the
general template
>>> dg.inputs.field_template = dict(struct='%s/struct.nii')
>>> dg.inputs.template_args['struct'] = [['sid']]
"""
input_spec = DataGrabberInputSpec
output_spec = DynamicTraitedSpec
_always_run = True
def __init__(self, infields=None, outfields=None, **kwargs):
"""
Parameters
----------
infields : list of str
Indicates the input fields to be dynamically created
outfields: list of str
Indicates output fields to be dynamically created
See class examples for usage
"""
if not outfields:
outfields = ['outfiles']
super(DataGrabber, self).__init__(**kwargs)
undefined_traits = {}
# used for mandatory inputs check
self._infields = infields
if infields:
for key in infields:
self.inputs.add_trait(key, traits.Any)
undefined_traits[key] = Undefined
# add ability to insert field specific templates
self.inputs.add_trait('field_template',
traits.Dict(traits.Enum(outfields),
desc="arguments that fit into template"))
undefined_traits['field_template'] = Undefined
if not isdefined(self.inputs.template_args):
self.inputs.template_args = {}
for key in outfields:
if not key in self.inputs.template_args:
if infields:
self.inputs.template_args[key] = [infields]
else:
self.inputs.template_args[key] = []
self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
def _add_output_traits(self, base):
"""
Using traits.Any instead out OutputMultiPath till add_trait bug
is fixed.
"""
return add_traits(base, self.inputs.template_args.keys())
def _list_outputs(self):
# infields are mandatory, however I could not figure out how to set 'mandatory' flag dynamically
# hence manual check
if self._infields:
for key in self._infields:
value = getattr(self.inputs,key)
if not isdefined(value):
msg = "%s requires a value for input '%s' because it was listed in 'infields'" % \
(self.__class__.__name__, key)
raise ValueError(msg)
outputs = {}
for key, args in self.inputs.template_args.items():
outputs[key] = []
template = self.inputs.template
if hasattr(self.inputs, 'field_template') and \
isdefined(self.inputs.field_template) and \
self.inputs.field_template.has_key(key):
template = self.inputs.field_template[key]
if isdefined(self.inputs.base_directory):
template = os.path.join(os.path.abspath(self.inputs.base_directory), template)
else:
template = os.path.abspath(template)
if not args:
filelist = glob.glob(template)
if len(filelist) == 0:
msg = 'Output key: %s Template: %s returned no files'%(key, template)
if self.inputs.raise_on_empty:
raise IOError(msg)
else:
warn(msg)
else:
if self.inputs.sort_filelist:
filelist.sort()
outputs[key] = list_to_filename(filelist)
for argnum, arglist in enumerate(args):
maxlen = 1
for arg in arglist:
if isinstance(arg, str) and hasattr(self.inputs, arg):
arg = getattr(self.inputs, arg)
if isinstance(arg, list):
if (maxlen > 1) and (len(arg) != maxlen):
raise ValueError('incompatible number of arguments for %s' % key)
if len(arg)>maxlen:
maxlen = len(arg)
outfiles = []
for i in range(maxlen):
argtuple = []
for arg in arglist:
if isinstance(arg, str) and hasattr(self.inputs, arg):
arg = getattr(self.inputs, arg)
if isinstance(arg, list):
argtuple.append(arg[i])
else:
argtuple.append(arg)
filledtemplate = template
if argtuple:
filledtemplate = template%tuple(argtuple)
outfiles = glob.glob(filledtemplate)
if len(outfiles) == 0:
msg = 'Output key: %s Template: %s returned no files'%(key, filledtemplate)
if self.inputs.raise_on_empty:
raise IOError(msg)
else:
warn(msg)
outputs[key].insert(i, None)
else:
if self.inputs.sort_filelist:
outfiles.sort()
outputs[key].insert(i,list_to_filename(outfiles))
if any([val==None for val in outputs[key]]):
outputs[key] = []
if len(outputs[key]) == 0:
outputs[key] = None
elif len(outputs[key]) == 1:
outputs[key] = outputs[key][0]
return outputs
class FSSourceInputSpec(BaseInterfaceInputSpec):
subjects_dir = Directory(mandatory=True,
desc='Freesurfer subjects directory.')
subject_id = traits.Str(mandatory=True,
desc='Subject name for whom to retrieve data')
hemi = traits.Enum('both', 'lh', 'rh', usedefault=True,
desc='Selects hemisphere specific outputs')
class FSSourceOutputSpec(TraitedSpec):
T1 = File(exists=True, desc='Intensity normalized whole-head volume', loc='mri')
aseg = File(exists=True, desc='Volumetric map of regions from automatic segmentation',
loc='mri')
brain = File(exists=True, desc='Intensity normalized brain-only volume', loc='mri')
brainmask = File(exists=True, desc='Skull-stripped (brain-only) volume', loc='mri')
filled = File(exists=True, desc='Subcortical mass volume', loc='mri')
norm = File(exists=True, desc='Normalized skull-stripped volume', loc='mri')
nu = File(exists=True, desc='Non-uniformity corrected whole-head volume', loc='mri')
orig = File(exists=True, desc='Base image conformed to Freesurfer space',
loc='mri')
rawavg = File(exists=True, desc='Volume formed by averaging input images',
loc='mri')
ribbon = OutputMultiPath(File(exists=True), desc='Volumetric maps of cortical ribbons',
loc='mri', altkey='*ribbon')
wm = File(exists=True, desc='Segmented white-matter volume', loc='mri')
wmparc = File(exists=True, desc='Aparc parcellation projected into subcortical white matter',
loc='mri')
curv = OutputMultiPath(File(exists=True), desc='Maps of surface curvature',
loc='surf')
inflated = OutputMultiPath(File(exists=True), desc='Inflated surface meshes',
loc='surf')
pial = OutputMultiPath(File(exists=True), desc='Gray matter/pia mater surface meshes',
loc='surf')
smoothwm = OutputMultiPath(File(exists=True), loc='surf',
desc='Smoothed original surface meshes')
sphere = OutputMultiPath(File(exists=True), desc='Spherical surface meshes',
loc='surf')
sulc = OutputMultiPath(File(exists=True), desc='Surface maps of sulcal depth', loc='surf')
thickness = OutputMultiPath(File(exists=True), loc='surf',
desc='Surface maps of cortical thickness')
volume = OutputMultiPath(File(exists=True), desc='Surface maps of cortical volume', loc='surf')
white = OutputMultiPath(File(exists=True), desc='White/gray matter surface meshes',
loc='surf')
label = OutputMultiPath(File(exists=True), desc='Volume and surface label files',
loc='label', altkey='*label')
annot = OutputMultiPath(File(exists=True), desc='Surface annotation files',
loc='label', altkey='*annot')
aparc_aseg = OutputMultiPath(File(exists=True), loc='mri', altkey='aparc*aseg',
desc='Aparc parcellation projected into aseg volume')
sphere_reg = OutputMultiPath(File(exists=True), loc='surf', altkey='sphere.reg',
desc='Spherical registration file')
aseg_stats = OutputMultiPath(File(exists=True), loc='stats', altkey='aseg',
desc='Automated segmentation statistics file')
wmparc_stats = OutputMultiPath(File(exists=True), loc='stats', altkey='wmparc',
desc='White matter parcellation statistics file')
aparc_stats = OutputMultiPath(File(exists=True), loc='stats', altkey='aparc',
desc='Aparc parcellation statistics files')
BA_stats = OutputMultiPath(File(exists=True), loc='stats', altkey='BA',
desc='Brodmann Area statistics files')
aparc_a2009s_stats = OutputMultiPath(File(exists=True), loc='stats', altkey='aparc.a2009s',
desc='Aparc a2009s parcellation statistics files')
curv_stats = OutputMultiPath(File(exists=True), loc='stats', altkey='curv',
desc='Curvature statistics files')
entorhinal_exvivo_stats = OutputMultiPath(File(exists=True), loc='stats', altkey='entorhinal_exvivo',
desc='Entorhinal exvivo statistics files')
class FreeSurferSource(IOBase):
"""Generates freesurfer subject info from their directories
Examples
--------
>>> from nipype.interfaces.io import FreeSurferSource
>>> fs = FreeSurferSource()
>>> #fs.inputs.subjects_dir = '.'
>>> fs.inputs.subject_id = 'PWS04'
>>> res = fs.run() # doctest: +SKIP
>>> fs.inputs.hemi = 'lh'
>>> res = fs.run() # doctest: +SKIP
"""
input_spec = FSSourceInputSpec
output_spec = FSSourceOutputSpec
def _get_files(self, path, key, dirval, altkey=None):
globsuffix = ''
if dirval == 'mri':
globsuffix = '.mgz'
elif dirval == 'stats':
globsuffix = '.stats'
globprefix = ''
if key == 'ribbon' or dirval in ['surf', 'label', 'stats']:
if self.inputs.hemi != 'both':
globprefix = self.inputs.hemi+'.'
else:
globprefix = '*'
if key == 'aseg_stats' or key == 'wmparc_stats':
globprefix = ''
keydir = os.path.join(path,dirval)
if altkey:
key = altkey
globpattern = os.path.join(keydir,''.join((globprefix,key,globsuffix)))
return glob.glob(globpattern)
def _list_outputs(self):
subjects_dir = self.inputs.subjects_dir
subject_path = os.path.join(subjects_dir, self.inputs.subject_id)
output_traits = self._outputs()
outputs = output_traits.get()
for k in outputs.keys():
val = self._get_files(subject_path, k,
output_traits.traits()[k].loc,
output_traits.traits()[k].altkey)
if val:
outputs[k] = list_to_filename(val)
return outputs
class XNATSourceInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
query_template = traits.Str(
mandatory=True,
desc=('Layout used to get files. Relative to base '
'directory if defined')
)
query_template_args = traits.Dict(
traits.Str,
traits.List(traits.List),
value=dict(outfiles=[]), usedefault=True,
desc='Information to plug into template'
)
server = traits.Str(
mandatory=True,
requires=['user', 'pwd'],
xor=['config']
)
user = traits.Str()
pwd = traits.Password()
config = File(mandatory=True, xor=['server'])
cache_dir = Directory(desc='Cache directory')
class XNATSource(IOBase):
""" Generic XNATSource module that wraps around the pyxnat module in
an intelligent way for neuroimaging tasks to grab files and data
from an XNAT server.
Examples
--------
>>> from nipype.interfaces.io import XNATSource
Pick all files from current directory
>>> dg = XNATSource()
>>> dg.inputs.template = '*'
>>> dg = XNATSource(infields=['project','subject','experiment','assessor','inout'])
>>> dg.inputs.query_template = '/projects/%s/subjects/%s/experiments/%s' \
'/assessors/%s/%s_resources/files'
>>> dg.inputs.project = 'IMAGEN'
>>> dg.inputs.subject = 'IMAGEN_000000001274'
>>> dg.inputs.experiment = '*SessionA*'
>>> dg.inputs.assessor = '*ADNI_MPRAGE_nii'
>>> dg.inputs.inout = 'out'
>>> dg = XNATSource(infields=['sid'],outfields=['struct','func'])
>>> dg.inputs.query_template = '/projects/IMAGEN/subjects/%s/experiments/*SessionA*' \
'/assessors/*%s_nii/out_resources/files'
>>> dg.inputs.query_template_args['struct'] = [['sid','ADNI_MPRAGE']]
>>> dg.inputs.query_template_args['func'] = [['sid','EPI_faces']]
>>> dg.inputs.sid = 'IMAGEN_000000001274'
"""
input_spec = XNATSourceInputSpec
output_spec = DynamicTraitedSpec
def __init__(self, infields=None, outfields=None, **kwargs):
"""
Parameters
----------
infields : list of str
Indicates the input fields to be dynamically created
outfields: list of str
Indicates output fields to be dynamically created
See class examples for usage
"""
super(XNATSource, self).__init__(**kwargs)
undefined_traits = {}
# used for mandatory inputs check
self._infields = infields
if infields:
for key in infields:
self.inputs.add_trait(key, traits.Any)
undefined_traits[key] = Undefined
self.inputs.query_template_args['outfiles'] = [infields]
if outfields:
# add ability to insert field specific templates
self.inputs.add_trait(
'field_template',
traits.Dict(traits.Enum(outfields),
desc="arguments that fit into query_template")
)
undefined_traits['field_template'] = Undefined
#self.inputs.remove_trait('query_template_args')
outdict = {}
for key in outfields:
outdict[key] = []
self.inputs.query_template_args = outdict
self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
def _add_output_traits(self, base):
"""
Using traits.Any instead out OutputMultiPath till add_trait bug
is fixed.
"""
return add_traits(base, self.inputs.query_template_args.keys())
def _list_outputs(self):
# infields are mandatory, however I could not figure out
# how to set 'mandatory' flag dynamically, hence manual check
cache_dir = self.inputs.cache_dir or tempfile.gettempdir()
if self.inputs.config:
xnat = pyxnat.Interface(config=self.inputs.config)
else:
xnat = pyxnat.Interface(self.inputs.server,
self.inputs.user,
self.inputs.pwd,
cache_dir
)
if self._infields:
for key in self._infields:
value = getattr(self.inputs,key)
if not isdefined(value):
msg = ("%s requires a value for input '%s' "
"because it was listed in 'infields'" % \
(self.__class__.__name__, key)
)
raise ValueError(msg)
outputs = {}
for key, args in self.inputs.query_template_args.items():
outputs[key] = []
template = self.inputs.query_template
if hasattr(self.inputs, 'field_template') and \
isdefined(self.inputs.field_template) and \
self.inputs.field_template.has_key(key):
template = self.inputs.field_template[key]
if not args:
file_objects = xnat.select(template).get('obj')
if file_objects == []:
raise IOError('Template %s returned no files' \
% template
)
outputs[key] = list_to_filename(
[str(file_object.get())
for file_object in file_objects
if file_object.exists()
])
for argnum, arglist in enumerate(args):
maxlen = 1
for arg in arglist:
if isinstance(arg, str) and hasattr(self.inputs, arg):
arg = getattr(self.inputs, arg)
if isinstance(arg, list):
if (maxlen > 1) and (len(arg) != maxlen):
raise ValueError('incompatible number '
'of arguments for %s' % key
)
if len(arg)>maxlen:
maxlen = len(arg)
outfiles = []
for i in range(maxlen):
argtuple = []
for arg in arglist:
if isinstance(arg, str) and \
hasattr(self.inputs, arg):
arg = getattr(self.inputs, arg)
if isinstance(arg, list):
argtuple.append(arg[i])
else:
argtuple.append(arg)
if argtuple:
target = template % tuple(argtuple)
file_objects = xnat.select(target).get('obj')
if file_objects == []:
raise IOError('Template %s '
'returned no files' % target
)
outfiles = list_to_filename(
[str(file_object.get())
for file_object in file_objects
if file_object.exists()
]
)
else:
file_objects = xnat.select(template).get('obj')
if file_objects == []:
raise IOError('Template %s '
'returned no files' % template
)
outfiles = list_to_filename(
[str(file_object.get())
for file_object in file_objects
if file_object.exists()
]
)
outputs[key].insert(i,outfiles)
if len(outputs[key]) == 0:
outputs[key] = None
elif len(outputs[key]) == 1:
outputs[key] = outputs[key][0]
return outputs
class XNATSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
_outputs = traits.Dict(traits.Str, value={}, usedefault=True)
server = traits.Str(mandatory=True,
requires=['user', 'pwd'],
xor=['config']
)
user = traits.Str()
pwd = traits.Password()
config = File(mandatory=True, xor=['server'])
cache_dir = Directory(desc='')
project_id = traits.Str(
desc='Project in which to store the outputs', mandatory=True)
subject_id = traits.Str(
desc='Set to subject id', mandatory=True)
experiment_id = traits.Str(
desc='Set to workflow name', mandatory=True)
assessor_id = traits.Str(
desc=('Option to customize ouputs representation in XNAT - '
'assessor level will be used with specified id'),
mandatory=False,
xor=['reconstruction_id']
)
reconstruction_id = traits.Str(
desc=('Option to customize ouputs representation in XNAT - '
'reconstruction level will be used with specified id'),
mandatory=False,
xor=['assessor_id']
)
share = traits.Bool(
desc=('Option to share the subjects from the original project'
'instead of creating new ones when possible - the created '
'experiments are then shared backk to the original project'
),
value=False,
usedefault=True,
mandatory=False,
)
def __setattr__(self, key, value):
if key not in self.copyable_trait_names():
self._outputs[key] = value
else:
super(XNATSinkInputSpec, self).__setattr__(key, value)
class XNATSink(IOBase):
""" Generic datasink module that takes a directory containing a
list of nifti files and provides a set of structured output
fields.
"""
input_spec = XNATSinkInputSpec
def _list_outputs(self):
"""Execute this module.
"""
# setup XNAT connection
cache_dir = self.inputs.cache_dir or tempfile.gettempdir()
if self.inputs.config:
xnat = pyxnat.Interface(config=self.inputs.config)
else:
xnat = pyxnat.Interface(self.inputs.server,
self.inputs.user,
self.inputs.pwd,
cache_dir
)
# if possible share the subject from the original project
if self.inputs.share:
result = xnat.select(
'xnat:subjectData',
['xnat:subjectData/PROJECT',
'xnat:subjectData/SUBJECT_ID']
).where('xnat:subjectData/SUBJECT_ID = %s AND' %
self.inputs.subject_id
)
subject_id = self.inputs.subject_id
# subject containing raw data exists on the server
if isinstance(result.data[0], dict):
result = result.data[0]
shared = xnat.select('/project/%s/subject/%s' %
(self.inputs.project_id,
self.inputs.subject_id
)
)
if not shared.exists(): # subject not in share project
share_project = xnat.select(
'/project/%s' % self.inputs.project_id)
if not share_project.exists(): # check project exists
share_project.insert()
subject = xnat.select('/project/%(project)s'
'/subject/%(subject_id)s' % result
)
subject.share(str(self.inputs.project_id))
else:
# subject containing raw data does not exist on the server
subject_id = '%s_%s' % (
quote_id(self.inputs.project_id),
quote_id(self.inputs.subject_id)
)
# setup XNAT resource
uri_template_args = {
'project_id':quote_id(self.inputs.project_id),
'subject_id':subject_id,
'experiment_id': '%s_%s_%s' % (
quote_id(self.inputs.project_id),
quote_id(self.inputs.subject_id),
quote_id(self.inputs.experiment_id)
)
}
if self.inputs.share:
uri_template_args['original_project'] = result['project']
if self.inputs.assessor_id:
uri_template_args['assessor_id'] = (
'%s_%s' % (
uri_template_args['experiment_id'],
quote_id(self.inputs.assessor_id)
)
)
elif self.inputs.reconstruction_id:
uri_template_args['reconstruction_id'] = (
'%s_%s' % (
uri_template_args['experiment_id'],
quote_id(self.inputs.reconstruction_id)
)
)
# gather outputs and upload them
for key, files in self.inputs._outputs.items():
for name in filename_to_list(files):
if isinstance(name, list):
for i, file_name in enumerate(name):
push_file(self, xnat, file_name,
'%s_' % i + key,
uri_template_args
)
else:
push_file(self, xnat, name, key, uri_template_args)
def quote_id(string):
return str(string).replace('_', '---')
def unquote_id(string):
return str(string).replace('---', '_')
def push_file(self, xnat, file_name, out_key, uri_template_args):
# grab info from output file names
val_list = [unquote_id(val)
for part in os.path.split(file_name)[0].split(os.sep)
for val in part.split('_')[1:]
if part.startswith('_') and len(part.split('_')) % 2
]
keymap = dict(zip(val_list[1::2],val_list[2::2]))
_label = []
for key, val in sorted(keymap.items()):
if str(self.inputs.subject_id) not in val:
_label.extend([key, val])
# select and define container level
uri_template_args['container_type'] = None
for container in ['assessor_id', 'reconstruction_id']:
if getattr(self.inputs, container):
uri_template_args['container_type'] = container.split('_id')[0]
uri_template_args['container_id'] = uri_template_args[container]
if uri_template_args['container_type'] is None:
uri_template_args['container_type'] = 'reconstruction'
uri_template_args['container_id'] = unquote_id(
uri_template_args['experiment_id']
)
if _label:
uri_template_args['container_id'] += (
'_results_%s' % '_'.join(_label)
)
else:
uri_template_args['container_id'] += '_results'
# define resource level
uri_template_args['resource_label'] = (
'%s_%s' % (uri_template_args['container_id'],
out_key.split('.')[0]
)
)
# define file level
uri_template_args['file_name'] = os.path.split(
os.path.abspath(unquote_id(file_name)))[1]
uri_template = (
'/project/%(project_id)s/subject/%(subject_id)s'
'/experiment/%(experiment_id)s/%(container_type)s/%(container_id)s'
'/out/resource/%(resource_label)s/file/%(file_name)s'
)
# unquote values before uploading
for key in uri_template_args.keys():
uri_template_args[key] = unquote_id(uri_template_args[key])
# upload file
remote_file = xnat.select(uri_template % uri_template_args)
remote_file.insert(file_name,
experiments='xnat:imageSessionData',
use_label=True
)
# shares the experiment back to the original project if relevant
if uri_template_args.has_key('original_project'):
experiment_template = (
'/project/%(original_project)s'
'/subject/%(subject_id)s/experiment/%(experiment_id)s'
)
xnat.select(experiment_template % uri_template_args
).share(uri_template_args['original_project'])
def capture_provenance():
pass
def push_provenance():
pass
class SQLiteSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
database_file = File(exists=True, mandatory = True)
table_name = traits.Str(mandatory=True)
class SQLiteSink(IOBase):
""" Very simple frontend for storing values into SQLite database.
.. warning::
This is not a thread-safe node because it can write to a common
shared location. It will not complain when it overwrites a file.
Examples
--------
>>> sql = SQLiteSink(input_names=['subject_id', 'some_measurement'])
>>> sql.inputs.database_file = 'my_database.db'
>>> sql.inputs.table_name = 'experiment_results'
>>> sql.inputs.subject_id = 's1'
>>> sql.inputs.some_measurement = 11.4
>>> sql.run() # doctest: +SKIP
"""
input_spec = SQLiteSinkInputSpec
def __init__(self, input_names, **inputs):
super(SQLiteSink, self).__init__(**inputs)
self._input_names = filename_to_list(input_names)
add_traits(self.inputs, [name for name in self._input_names])
def _list_outputs(self):
"""Execute this module.
"""
conn = sqlite3.connect(self.inputs.database_file,
check_same_thread = False)
c = conn.cursor()
c.execute("INSERT OR REPLACE INTO %s (" % self.inputs.table_name +
",".join(self._input_names) + ") VALUES (" +
",".join(["?"]*len(self._input_names)) + ")",
[getattr(self.inputs,name) for name in self._input_names])
conn.commit()
c.close()
return None
|