ENH: Adding brains module

ENH: Added segmentation volume support

ENH: Added posterior volume support

AutoWorkup/brains/__init__.py

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+__version__ = 'beta'
+#import config
+#import metrics
+
+def check_file(filename):
+    import os.path
+    fullName = os.path.abspath(filename)
+    assert os.path.exists(fullName), "File %s cannot be found!" % fullName
+    return fullName

AutoWorkup/brains/config/__init__.py

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+from ConfigParser import SafeConfigParser as scp
+_config = scp()
+
+from autoworkup import *

AutoWorkup/brains/config/autoworkup.py

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+from . import _config
+
+valid_schemes = ['BRAINS', 'Nipype']
+
+def writeConfiguration(filename='example.config'):
+    config = ConfigParser.SafeConfigParser()
+    config.add_section("Results")
+    config.set("Results", "directory", "/full/path/to/experiment/directory")
+    config.set("Results", "segmentations", "SingleRFSegmentations")
+    config.set("Results", "posteriors", "TissueClassify")
+    config.set("Results", "scheme", "BRAINS")
+    with open(filename, 'wb') as configfile:
+        config.write(configfile)
+
+
+def loadConfiguration(configFile='/dev/null'):
+    _config.read(configFile)
+
+#_config = loadConfiguration()

AutoWorkup/brains/metrics/__init__.py

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+from ..config import loadConfiguration
+from segmentations import *
+from partials import *
+
+

AutoWorkup/brains/metrics/partials.py

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+import numpy as np
+import os.path
+from warnings import warn
+
+import SimpleITK as sitk
+
+from ..config import _config
+
+posteriors = ['accumben', 'air', 'caudate', 'crblgm', 'crblwm', 'csf', 'globus', 'hippocampus', 'notcsf', 'notgm', 'notvb', 'notwm', 'putamen', 'surfgm', 'thalamus', 'vb', 'wm']
+_tolerance = [0.99, 1.01]
+_tolerance_wm = [0.99, 1.01]
+
+
+def _formatPosteriorAssertString():
+    assertString = "Posterior label is not recognized: %s\nValid labels are:"
+    for p in posteriors:
+        assertString = '\n'.join([assertString, p.upper() + ','])
+    assertString = assertString[:-1]
+    return assertString
+
+
+def _checkPosteriorLabel(label):
+    errorString = _formatPosteriorAssertString()
+    assert label.lower() in posteriors, errorString % label
+
+
+def calculateBinaryVolume(dirname, label):
+    label = label.upper()
+    _checkPosteriorLabel(label)
+    labelFile = os.path.join(dirname, 'POSTERIOR_'+ label + '.nii.gz')
+    assert os.path.exists(labelFile), "File not found: %s" % labelFile
+    image = sitk.ReadImage(labelFile)
+    if label == 'WM':
+        lowerTol, upperTol = _tolerance_wm
+        warn("Using lower threshold of %g for white matter binary calculations." % lowerTol)
+    else:
+        lowerTol, upperTol = _tolerance
+    binary = sitk.BinaryThreshold(image, lowerTol, upperTol, 1, 0)
+    nda = sitk.GetArrayFromImage(binary)
+    maskSum = nda.sum()
+    ## print maskSum
+    size = image.GetSpacing()
+    ## print size
+    return maskSum * size[0] * size[1] * size[2]
+
+
+def calculatePartialVolume(dirname, label):
+    label = label.upper()
+    _checkPosteriorLabel(label)
+    labelFile = os.path.join(dirname, 'POSTERIOR_' + label + '.nii.gz')
+    assert os.path.exists(labelFile), "File not found: %s" % labelFile
+    image = sitk.ReadImage(labelFile)
+    nda = sitk.GetArrayFromImage(image)
+    maskSum = nda.sum()
+    ## print maskSum
+    size = image.GetSpacing()
+    ## print size
+    return maskSum * size[0] * size[1] * size[2]
+
+
+def getPartialVolume(args=[], kwds={}):
+    dirname = labels = project = subject = session = experimentDir = None
+    experimentDir = _config.get('Results', 'directory')
+    partialsDir = _config.get('Results', 'posteriors')
+    for key, value in kwds:
+        if key == 'dirname':
+            dirname = check_file(value)
+        elif key == 'labels':
+            labels = value
+        elif key == 'project':
+            project = value
+        elif key == 'subject':
+            subject = value
+        elif key == 'session':
+            session = value
+    if session is None:
+        session = args.pop()
+    if subject is None:
+        subject = args.pop()
+    if project is None:
+        project = args.pop()
+    if labels is None:
+        labels = args
+    if dirname is None:
+        try:
+            dirname = os.path.join(experimentDir, project, subject, session, partialsDir)
+        except Exception, err:
+            raise err
+    ### DEBUGGING ###
+    #print labels
+    #print dirname
+    #print project
+    #print subject
+    #print session
+    ### END DEBUG ###
+    # labels = map(formatLabel, labels) # convert shorthand to human-readable
+    volume = 0.0
+    for label in labels:
+        volume += calculateBinaryVolume(dirname, label)
+    return volume
+

AutoWorkup/brains/metrics/segmentations.py

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+import numpy as np
+import os.path
+
+import SimpleITK as sitk
+
+from ..config import _config
+labels = ['caudate', 'putamen', 'hippocampus', 'thalamus', 'accumben', 'globus']
+
+def constructLabels(labels):
+    numbers = range(1,((len(labels)*2) + 1))
+    full_labels = []
+    index = 0
+    for label in labels:
+        full_labels.append('_'.join(['left', label]))
+        full_labels.append('_'.join(['right', label]))
+    return full_labels, numbers
+
+def _moduleCreateLabels(labels):
+    full_labels, numbers = constructLabels(labels)
+    labelMap = map(None, full_labels, numbers)
+    return dict(labelMap) # Use this variable
+
+
+def formatLabel(label):
+    """
+    Assumes that the label can be split by the '_' character.
+    """
+    side, anatomy = label.split('_')
+    if side.lower() in ['l', 'left']:
+        side = 'left'
+    elif side.lower() in ['r', 'right']:
+        side = 'right'
+    else:
+        raise ValueError('Label %s is not recognized: cannot determine side %s' % (label, side))
+    label = '_'.join([side,anatomy])
+    return label
+
+
+def calculateLabelVolume(dirname, label):
+    labelFile = os.path.join(dirname, _config.get('Results', 'segmentations'), label + '_seg.nii.gz')
+    assert os.path.exists(labelFile), "File not found: %s" % labelFile
+    image = sitk.ReadImage(labelFile)
+    nda = sitk.GetArrayFromImage(image)
+    maskSum = nda.sum()
+    print maskSum
+    size = image.GetSpacing()
+    print size
+    return maskSum * size[0] * size[1] * size[2]
+
+
+def getVolume(args=[], kwds={}):
+    dirname = labels = project = subject = session = experimentDir = None
+    experimentDir = _config.get('Results', 'directory') ### HACK
+    for key, value in kwds:
+        if key == 'dirname':
+            dirname = check_file(value)
+        elif key == 'labels':
+            labels = value
+        elif key == 'project':
+            project = value
+        elif key == 'subject':
+            subject = value
+        elif key == 'session':
+            session = value
+    if session is None:
+        session = args.pop()
+    if subject is None:
+        subject = args.pop()
+    if project is None:
+        project = args.pop()
+    if labels is None:
+        labels = args
+    if dirname is None:
+        try:
+        # config needs to be accessible
+            dirname = os.path.join(experimentDir, project, subject, session)
+        except Exception, err:
+            raise err
+    ### DEBUGGING ###
+    #print labels
+    #print dirname
+    #print project
+    #print subject
+    #print session
+    ### END DEBUG ###
+    # labels = map(formatLabel, labels) # convert shorthand to human-readable
+    volume = 0.0
+    for label in labels:
+        volume += calculateLabelVolume(dirname, label)
+    return volume