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)
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)
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
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)
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_())
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)
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])
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
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)
#!/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_()
#!/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_()
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)
