Esempio n. 1
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def build_graph(subjects, database, types, verbose=True):
    from brainvisa import axon
    axon.initializeProcesses()
    import neuroHierarchy
    db = neuroHierarchy.databases.database(osp.abspath(database))

    dates = {}
    lines = [], []
    steps = []
    for i, s in enumerate(subjects):
        if verbose and False:
            print s, '(%s/%s)'%(i, len(subjects))
        dates[s] = get_subject_dates(s, db, types)
        stypes = [types.index(e) for e in dates[s].keys()]
        ordered_dates = [dates[s][types[k]] for k in stypes]
        if len(stypes) == 0:
            print 'no items found for subject', s
            continue
        lines[0].extend(pd.to_datetime([datetime.fromtimestamp(e) for e in ordered_dates]))
        lines[1].extend([i]*len(ordered_dates))
        steps.extend(stypes)


    l0, l1 = {}, {}
    for x, y ,label in zip(lines[0], lines[1], steps):
        l0.setdefault(label, []).append(x)
        l1.setdefault(label, []).append(y)

    legends = [types[i] for i in set(steps)]
    plot(subjects, l0, l1, steps, legends)
Esempio n. 2
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def build_graph(subjects, database, types, verbose=True):
    from brainvisa import axon
    axon.initializeProcesses()
    import neuroHierarchy
    db = neuroHierarchy.databases.database(osp.abspath(database))

    dates = {}
    lines = [], []
    steps = []
    for i, s in enumerate(subjects):
        if verbose and False:
            print s, '(%s/%s)' % (i, len(subjects))
        dates[s] = get_subject_dates(s, db, types)
        stypes = [types.index(e) for e in dates[s].keys()]
        ordered_dates = [dates[s][types[k]] for k in stypes]
        if len(stypes) == 0:
            print 'no items found for subject', s
            continue
        lines[0].extend(
            pd.to_datetime([datetime.fromtimestamp(e) for e in ordered_dates]))
        lines[1].extend([i] * len(ordered_dates))
        steps.extend(stypes)

    l0, l1 = {}, {}
    for x, y, label in zip(lines[0], lines[1], steps):
        l0.setdefault(label, []).append(x)
        l1.setdefault(label, []).append(y)

    legends = [types[i] for i in set(steps)]
    plot(subjects, l0, l1, steps, legends)
Esempio n. 3
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def check_subject(subject, database, jsonfile, antecfile, verbose=True):
    ''' Given a subject, the path to a database and a JSON file describing
    input/outputs of a pipeline, checks'''
    from brainvisa import axon
    axon.initializeProcesses()
    import neuroHierarchy
    db = neuroHierarchy.databases.database(osp.abspath(database))
    j = json.load(open(jsonfile))
    types = json.load(open(antecfile))  #collect_types(jsonfile)
    dates = get_subject_dates(subject, db, types)

    issues = []
    for k, v in j.items():
        outputs = [e.strip('>') for e in v if e.startswith('>')]
        inputs = [e.strip('@') for e in v if e.startswith('@')]
        for i in inputs:
            for o in outputs:
                if o in dates and i in dates:
                    if dates[o] < dates[i]:
                        if verbose:
                            print 'problem with', o, '(%s)' % datetime.fromtimestamp(
                                dates[o]), i, '(%s)' % datetime.fromtimestamp(
                                    dates[i]), subject, k
                        issues.append(
                            (o, datetime.fromtimestamp(dates[o]), i,
                             datetime.fromtimestamp(dates[i]), subject, k))
    return issues
Esempio n. 4
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def identify_tissues_axon(subject, database='/home/grg/data/ALFA_DWI', doit=False, verbose=True):
    from brainvisa import axon
    axon.initializeProcesses()
    import neuroHierarchy
    db = neuroHierarchy.databases._databases[database]
    fast = [e for e in db.findDiskItems(_type='ALFA DWI B0 Brain FSL FAST', subject=subject)][0].fullPath()
    b0 = [e for e in db.findDiskItems(_type='ALFA DWI B0 Map', subject=subject)][0].fullPath()
    identify_tissues(fast, b0, doit, verbose)
Esempio n. 5
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def main(noapp=0):
    app = None
    if noapp == 0:
        print "NO APP"
        app = QtGui.QApplication(sys.argv)
        axon.initializeProcesses()
        ll = LocateLeds(app=app)
        ll.show()

    if noapp == 0:
        sys.exit(app.exec_())
Esempio n. 6
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def backup_freesurfer_subject(subject, tarfile, dbdir, doit=False, verbose=True):
    from brainvisa import axon
    axon.initializeProcesses()
    import neuroHierarchy
    db = neuroHierarchy.databases._databases[dbdir]
    tmpdir = tempfile.mkdtemp()
    if not doit:
        print '##############################################'
        print 'Not doing the job. Just printing the commands.'
        print '##############################################'

    fstypes = ['ResampledWhite', 'ResampledPial', 'ResampledFreesurferThicknessType', 'Freesurfer Cortical Parcellation using Destrieux Atlas', 'Freesurfer aseg']
    if verbose:
        print '=== Collecting data for subject', subject, ' ==='

    for each in fstypes[0:3]:
        for side in ['left', 'right']:
            item = [e for e in db.findDiskItems(_type = each, subject=subject, side=side)]
            if len(item)!=1:
                raise Exception(' Expected one item of type %s found %s (%s)'%(each, len(item), ' - '.join([e.fullPath() for e in item])))
            copy_item(item[0], tmpdir, doit, verbose)
            if verbose:
                print each, side, item

    for each in fstypes[3:]:
        item = [e for e in db.findDiskItems(_type = each, subject=subject)]
        if len(item)!=1:
            raise Exception(' Expected one item of type %s found %s (%s)'%(each, len(item), ' - '.join([e.fullPath() for e in item])))
        copy_item(item[0], tmpdir, doit, verbose)
        print each, item

    mri = [e for e in db.findDiskItems(_type='T1 FreesurferAnat', _format='NIFTI-1 image', subject=subject)]
    if len(mri)!=1:
        raise Exception(' Expected one item of type %s found %s (%s)'%(each, len(item), ' - '.join([e.fullPath() for e in mri])))
    copy_item(mri[0], tmpdir, doit, verbose)
    print 'mri', mri

    opt = 'cvf'
    if osp.splitext(tarfile)[1] == '.gz':
        opt = opt + 'z'
    elif osp.splitext(tarfile)[1] != '.tar':
        tarfile = tarfile + '.tar'
    if verbose:
        print 'Creating %s'%tarfile
    p1, p2 = tmpdir, subject
    cmd = 'tar %s %s -C %s %s'%(opt, tarfile, p1, p2)
    if verbose:
        print cmd
    if doit:
        os.system(cmd)
Esempio n. 7
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    def run(self, directory):
        import os.path as osp
        directory = osp.abspath(directory)
        from brainvisa import axon
        axon.initializeProcesses()
        import neuroHierarchy
        for direct, db in neuroHierarchy.databases._databases.items():
            if direct == directory:
               break
        if direct != directory:
            raise Exception('%s should be a valid Axon database.\nCurrent'\
                    'existing Axon databases : %s'\
                    %(directory, neuroHierarchy.databases._databases.keys()))

        items = [each for each in db.findDiskItems(**{'_type': 'Any Type'})]

        self.identified = {}
        self.index = []
        self.firstcol = 'subject'

        self.headers = set()

        for each in items:
            subject = each.get(self.firstcol)
            self.index.append(subject)
            self.identified.setdefault(subject, {})
            self.headers.add(each.type.name)
            fp = each.fullPath()
            self.identified[subject].setdefault(each.type.name, []).append(fp)

        self.index = sorted(list(set(self.index)))
        self.headers = sorted(list(self.headers))
        self.repository = directory

        self.count_table = []
        self.table = []

        for s in self.index:
          h = self.headers
          self.count_table.append([len(self.identified[s].get(e, [])) for e in h])
          self.table.append([self.identified[s].get(e, []) for e in h])
Esempio n. 8
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def check_subject(subject, database, jsonfile, antecfile, verbose=True):
    ''' Given a subject, the path to a database and a JSON file describing
    input/outputs of a pipeline, checks'''
    from brainvisa import axon
    axon.initializeProcesses()
    import neuroHierarchy
    db = neuroHierarchy.databases.database(osp.abspath(database))
    j = json.load(open(jsonfile))
    types = json.load(open(antecfile)) #collect_types(jsonfile)
    dates = get_subject_dates(subject, db ,types)

    issues = []
    for k,v in j.items():
        outputs = [e.strip('>') for e in v if e.startswith('>')]
        inputs = [e.strip('@') for e in v if e.startswith('@')]
        for i in inputs:
            for o in outputs:
                if o in dates and i in dates:
                    if dates[o] < dates[i]:
                       if verbose:
                           print 'problem with', o,'(%s)'%datetime.fromtimestamp(dates[o]), i, '(%s)'%datetime.fromtimestamp(dates[i]), subject,k
                       issues.append((o, datetime.fromtimestamp(dates[o]), i, datetime.fromtimestamp(dates[i]), subject, k))
    return issues
Esempio n. 9
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def backup_subject_axon(subject,
                        tarfile,
                        database,
                        doit=False,
                        verbose=True,
                        remove=False):
    from brainvisa import axon
    axon.initializeProcesses()
    import neuroHierarchy
    db = neuroHierarchy.databases._databases[database]
    items = [e for e in db.findDiskItems(_type='Any Type', subject=subject)]
    items = [e.fullPath() for e in items if e.get('subject')]

    tmpdir = osp.join(tempfile.mkdtemp(), osp.split(database)[1])
    action = 'cp' if not remove else 'mv'

    if verbose:
        print 'Found %s items' % len(items)
        print items

    if not doit:
        print '##############################################'
        print 'Not doing the job. Just printing the commands.'
        print '##############################################'

    for i in items:
        f = i.split(database)[1][1:]
        newdir = osp.join(tmpdir, osp.split(f)[0])
        if not osp.isdir(newdir):
            cmd = 'super-mkdir %s' % newdir
            if verbose:
                print cmd
            if doit:
                os.makedirs(newdir)
        cmd = 'cp %s %s' % (i, osp.join(tmpdir, f))
        if verbose:
            print cmd
        if doit:
            os.system(cmd)

        if remove:
            db.removeDiskItem(db.createDiskItemFromFilename(i),
                              eraseFiles=True)

    if action == 'mv':
        removed = 0
        for i in items:
            if not osp.exists(i):
                removed += 1
        if verbose:
            print 'Removed %s files out of %s' % (removed, len(items))
            emptydirs = list(find_empty_dirs(database))
            print len(emptydirs), 'empty directories in %s (%s)' % (
                database, ', '.join(emptydirs))

    opt = 'cvf'
    if osp.splitext(tarfile)[1] == '.gz':
        opt = opt + 'z'
    elif osp.splitext(tarfile)[1] != '.tar':
        tarfile = tarfile + '.tar'
    if verbose:
        print 'Creating %s' % tarfile
    p1, p2 = osp.split(tmpdir)
    cmd = 'tar %s %s -C %s %s' % (opt, tarfile, p1, p2)
    if verbose:
        print cmd
    if doit:
        os.system(cmd)
Esempio n. 10
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#!/usr/bin/env python

import argparse

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Axon database browser')
    opts = parser.parse_args()

    from brainvisa import axon, processes

    axon.initializeProcesses()
    from brainvisa.data.qtgui.hierarchyBrowser import HierarchyBrowser
    from PyQt4 import QtGui, QtCore, Qt
    import sys

    app = Qt.QApplication(sys.argv)
    a = HierarchyBrowser()
    a.show()
    app.exec_()
Esempio n. 11
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#!/usr/bin/env python

import argparse

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Axon database browser')
    opts = parser.parse_args()

    from brainvisa import axon, processes

    axon.initializeProcesses()
    from brainvisa.data.qtgui.hierarchyBrowser import HierarchyBrowser
    from PyQt4 import QtGui, QtCore, Qt
    import sys

    app = Qt.QApplication( sys.argv )
    a = HierarchyBrowser()
    a.show()
    app.exec_()

Esempio n. 12
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def backup_subject_axon(subject, tarfile, database, doit=False, verbose=True, remove=False):
    from brainvisa import axon
    axon.initializeProcesses()
    import neuroHierarchy
    db = neuroHierarchy.databases._databases[database]
    items = [e for e in db.findDiskItems(_type='Any Type', subject=subject)]
    items = [e.fullPath() for e in items if e.get('subject')]

    tmpdir = osp.join(tempfile.mkdtemp(), osp.split(database)[1])
    action = 'cp' if not remove else 'mv'


    if verbose:
        print 'Found %s items'%len(items)
        print items

    if not doit:
        print '##############################################'
        print 'Not doing the job. Just printing the commands.'
        print '##############################################'

    for i in items:
        f = i.split(database)[1][1:]
        newdir = osp.join(tmpdir, osp.split(f)[0])
        if not osp.isdir(newdir):
            cmd = 'super-mkdir %s'%newdir
            if verbose:
                print cmd
            if doit:
                os.makedirs(newdir)
        cmd = 'cp %s %s'%(i, osp.join(tmpdir, f))
        if verbose:
            print cmd
        if doit:
            os.system(cmd)

        if remove:
            db.removeDiskItem(db.createDiskItemFromFilename(i), eraseFiles=True)


    if action == 'mv':
        removed = 0
        for i in items:
            if not osp.exists(i):
                removed += 1
        if verbose:
            print 'Removed %s files out of %s'%(removed, len(items))
	    emptydirs = list(find_empty_dirs(database))
	    print len(emptydirs), 'empty directories in %s (%s)'%(database, ', '.join(emptydirs))

    opt = 'cvf'
    if osp.splitext(tarfile)[1] == '.gz':
        opt = opt + 'z'
    elif osp.splitext(tarfile)[1] != '.tar':
        tarfile = tarfile + '.tar'
    if verbose:
        print 'Creating %s'%tarfile
    p1, p2 = osp.split(tmpdir)
    cmd = 'tar %s %s -C %s %s'%(opt, tarfile, p1, p2)
    if verbose:
        print cmd
    if doit:
        os.system(cmd)