def handle(self, signum, frame):
"""This method is called when a signal is received."""
if self.print_method:
self.print_method('\nProgram received signal %s'
% self.signame)
if self.print_stack:
import traceback
strings = traceback.format_stack(frame)
for s in strings:
if s[-1] == '\n': s = s[0:-1]
self.print_method(s)
if self.pass_along:
# pass the signal to the program
if self.old_handler:
self.old_handler(signum, frame)
if self.stop_method is not None:
## FIXME not sure if this is really right
if frame.f_trace is None:
import pydb
pydb.debugger()
else:
self.stop_method(frame)
pass
pass
return
def handle(self, signum, frame):
"""This method is called when a signal is received."""
if self.print_method:
self.print_method('\nProgram received signal %s' %
self.signame)
if self.print_stack:
import traceback
strings = traceback.format_stack(frame)
for s in strings:
if s[-1] == '\n': s = s[0:-1]
self.print_method(s)
if self.pass_along:
# pass the signal to the program
if self.old_handler:
self.old_handler(signum, frame)
if self.stop_method is not None:
## FIXME not sure if this is really right
if frame.f_trace is None:
import pydb
pydb.debugger()
else:
self.stop_method(frame)
pass
pass
return
def getOtherOperand(opNode, oneOperand):
if fileId == "qx.data.marshal.Json":
import pydb; pydb.debugger()
operands = opNode.getChildren(True)
#if operands[0] == oneOperand.parent: # switch between "first" and "second"
if operands[0] == oneOperand: # switch between "first" and "second"
#otherOperand = operands[1].getFirstChild(ignoreComments=True)
otherOperand = operands[1]
otherPosition = 1
else:
#otherOperand = operands[0].getFirstChild(ignoreComments=True)
otherOperand = operands[0]
otherPosition = 0
return otherOperand, otherPosition
def processVariantGet(callNode, variantMap):
treeModified = False
# Simple sanity checks
params = callNode.getChild("arguments")
if len(params.children) != 1:
log(
"Warning",
"Expecting exactly one argument for qx.core.Environment.get. Ignoring this occurrence.",
params)
return treeModified
firstParam = params.getChildByPosition(0)
if not isStringLiteral(firstParam):
# warning is currently covered in parsing code
#log("Warning", "First argument must be a string literal! Ignoring this occurrence.", firstParam)
return treeModified
# skipping "relative" calls like "a.b.qx.core.Environment.get()"
#(with the new ast and the isEnvironmentCall check, this cannot happen anymore)
#qxIdentifier = treeutil.selectNode(callNode, "operand/variable/identifier[1]")
#if not treeutil.checkFirstChainChild(qxIdentifier):
# log("Warning", "Skipping relative qx.core.Environment.get call. Ignoring this occurrence ('%s')." % treeutil.findChainRoot(qxIdentifier).toJavascript())
# return treeModified
variantKey = firstParam.get("value")
if variantKey in variantMap:
confValue = variantMap[variantKey]
else:
return treeModified
if variantKey == "qx.debug.databinding" and fileId == "qx.data.marshal.Json":
import pydb
pydb.debugger()
# Replace the .get() with its value
resultNode = reduceCall(callNode, confValue)
treeModified = True
# Reduce any potential operations with literals (+3, =='hugo', ?a:b, ...)
treeMod = True
while treeMod:
resultNode, treeMod = reduceOperation(resultNode)
# Reduce a potential condition
_ = reduceLoop(resultNode)
return treeModified
def processVariantGet(callNode, variantMap):
treeModified = False
# Simple sanity checks
params = callNode.getChild("arguments")
if len(params.children) != 1:
log("Warning", "Expecting exactly one argument for qx.core.Environment.get. Ignoring this occurrence.", params)
return treeModified
firstParam = params.getChildByPosition(0)
if not isStringLiteral(firstParam):
# warning is currently covered in parsing code
#log("Warning", "First argument must be a string literal! Ignoring this occurrence.", firstParam)
return treeModified
# skipping "relative" calls like "a.b.qx.core.Environment.get()"
#(with the new ast and the isEnvironmentCall check, this cannot happen anymore)
#qxIdentifier = treeutil.selectNode(callNode, "operand/variable/identifier[1]")
#if not treeutil.checkFirstChainChild(qxIdentifier):
# log("Warning", "Skipping relative qx.core.Environment.get call. Ignoring this occurrence ('%s')." % treeutil.findChainRoot(qxIdentifier).toJavascript())
# return treeModified
variantKey = firstParam.get("value");
if variantKey in variantMap:
confValue = variantMap[variantKey]
else:
return treeModified
if variantKey =="qx.debug.databinding" and fileId == "qx.data.marshal.Json":
import pydb; pydb.debugger()
# Replace the .get() with its value
resultNode = reduceCall(callNode, confValue)
treeModified = True
# Reduce any potential operations with literals (+3, =='hugo', ?a:b, ...)
treeMod = True
while treeMod:
resultNode, treeMod = reduceOperation(resultNode)
# Reduce a potential condition
_ = reduceLoop(resultNode)
return treeModified
#else:
# out += ','.join([l.text for l in labels])
#try:
output.write(out % voxel + "\n")
#except:
# import pydb
# pydb.debugger()
if args.dumpmapFile:
try:
ni_dump_data[coord_orig[0], coord_orig[1], coord_orig[2]] = \
[voxel['labels'][i]['label'].index
for i,ind in enumerate(args.levels)]
except Exception, e:
import pydb
pydb.debugger()
# if we opened any file -- close it
if fileIn:
fileIn.close()
if args.dumpmapFile:
ni_dump = nb.Nifti1Image(ni_dump_data, None, ni_dump.get_header())
ni_dump.to_filename(args.dumpmapFile)
if args.createSummary:
if numVoxels == 0:
verbose(1, "No matching voxels were found.")
else:
get_summary(args, summary, output)
#else:
# out += ','.join([l.text for l in labels])
#try:
output.write(out % voxel + "\n")
#except:
# import pydb
# pydb.debugger()
if args.dumpmapFile:
try:
ni_dump_data[coord_orig[0], coord_orig[1], coord_orig[2]] = \
[voxel['labels'][i]['label'].index
for i,ind in enumerate(args.levels)]
except Exception, e:
import pydb
pydb.debugger()
# if we opened any file -- close it
if fileIn:
fileIn.close()
if args.dumpmapFile:
ni_dump = nb.Nifti1Image(ni_dump_data, None, ni_dump.get_header())
ni_dump.to_filename(args.dumpmapFile)
if args.createSummary:
if numVoxels == 0:
verbose(1, "No matching voxels were found.")
else:
get_summary(args, summary, output)
"""Test to see if handles an exception when an error is raised."""
import os, sys
top_builddir = ".."
if top_builddir[-1] != os.path.sep:
top_builddir += os.path.sep
sys.path.insert(0, os.path.join(top_builddir, 'pydb'))
top_srcdir = ".."
if top_srcdir[-1] != os.path.sep:
top_srcdir += os.path.sep
sys.path.insert(0, os.path.join(top_srcdir, 'pydb'))
print __doc__
import pydb
pydb.debugger() # we go into the debugger
print "Returning from the debugger"
# Set a variable so we can show the state is
# somewhere after the above set_trace()
z='After set_trace'
try:
# The below statement should not enter the debugger
x=2/0
except:
pass
# We should enter the debugger on the next statement.
y=1/0 # Bullwinkle: This time, for sure!
pass
#!/usr/bin/python
"""Towers of Hanoi - testing calling debugger with continue and cmds"""
import sys
sys.path.insert(0, '..')
import pydb
pydb.debugger(dbg_cmds=['set basename on', 'set linetrace on', 'step 20'])
def hanoi(n, a, b, c):
if n - 1 > 0:
hanoi(n - 1, a, c, b)
print "Move disk %s to %s" % (a, b)
if n - 1 > 0:
hanoi(n - 1, c, b, a)
if __name__ == '__main__':
i_args = len(sys.argv)
if i_args != 1 and i_args != 2:
print "*** Need number of disks or no parameter"
sys.exit(1)
n = 3
sys.settrace(None)
if i_args > 1:
try:
n = int(sys.argv[1])
except ValueError, msg:
print "** Expecting an integer, got: %s" % repr(sys.argv[1])
if i_args > 3:
print "usage %s [disks [cmdfile]]" % sys.argv[0]
sys.exit(1)
n=3
if i_args > 1:
try:
n = int(sys.argv[1])
except ValueError, msg:
print "** Expecting an integer, got: %s" % repr(sys.argv[1])
sys.exit(2)
if n < 1 or n > 100:
print "*** number of disks should be between 1 and 100"
sys.exit(2)
dbg_cmds=['set basename on',
'where',
'list',
'step',
'step',
'where',
'info locals',
'set linetrace on',
'continue']
import pydb
pydb.debugger(dbg_cmds)
hanoi(n, "a", "b", "c")
def main():
# XXX: I cannot figure out why I have to re-import `os`
# here; it has already been imported at the start of the
# file ...
import os
# disable core dumps
resource.setrlimit(resource.RLIMIT_CORE, (0,0))
# parse command-line options
import argparse
parser = argparse.ArgumentParser(
description="""
Actions:
graphs G N
Generate the graphs occurring in M_{g,n}.
homology G N
Print homology ranks of M_{g,n}.
latex G N [-s DIR] [-o FILE]
Read the listings of M_{g,n} fatgraphs (from directory DIR)
and output a pretty-print catalogue of the graphs as LaTeX documents.
valences G N
Print the vertex valences occurring in M_{g,n} graphs.
shell
Start an interactive PyDB shell.
selftest
Run internal code tests and report failures.
""",
formatter_class=argparse.RawTextHelpFormatter)
# positional arguments
parser.add_argument('action', metavar='ACTION', default='help',
help="Action to perform, see above.")
parser.add_argument('args', metavar='ARG', nargs='*',
help="Arguments depend on the actual action, see above.")
# option arguments
if not cython_compiled:
parser.add_argument("-D", "--debug", nargs='?',
dest="debug", default=None, const='debug',
help="""Enable debug features:
* pydb -- run Python debugger if an error occurs
* profile -- dump profiler statistics in a .pf file.
Several features may be enabled by separating them
with a comma, as in '-D pydb,profile'.""")
parser.add_argument("-l", "--logfile",
action='store', dest='logfile', default=None,
help="""Redirect log messages to the named file
(by default log messages are output to STDERR).""")
parser.add_argument("-o", "--output", dest="outfile", default=None,
help="Save results into named file.")
parser.add_argument("-s", "--checkpoint", dest="checkpoint_dir", default=None,
help="Directory for saving computation state.")
parser.add_argument("-u", "--afresh", dest="restart", action="store_false", default=True,
help="Do NOT restart computation from the saved state in checkpoint directory.")
parser.add_argument("-v", "--verbose",
action="count", dest="verbose", default=0,
help="Print informational and status messages as the computation goes on.")
parser.add_argument('-V', '--version', action='version', version=__version__)
cmdline = parser.parse_args()
# make options available to loaded modules
runtime.options = cmdline
# print usage message if no args given
if 'help' == cmdline.action:
parser.print_help()
sys.exit(0)
# configure logging
if cmdline.logfile is None:
log_output = sys.stderr
else:
log_output = file(cmdline.logfile, 'a')
if cmdline.verbose == 0:
log_level = logging.ERROR
elif cmdline.verbose == 1:
log_level = logging.INFO
else:
log_level = logging.DEBUG
logging.basicConfig(level=log_level,
stream=log_output,
format="%(asctime)s [%(levelname)s] %(message)s",
datefmt="%H:%M:%S")
# ensure the proper optimization level is selected
if __debug__ and cmdline.debug is None:
try:
os.execl(sys.executable, *([sys.executable, '-O'] + sys.argv))
finally:
logging.warning("Could not execute '%s', ignoring '-O' option."
% str.join(" ", [sys.executable, '-O'] + sys.argv))
# enable optional features
if not cython_compiled and cmdline.debug is not None:
debug = cmdline.debug.split(",")
if 'pydb' in debug:
try:
import pydb
sys.excepthook = pydb.exception_hook
logging.debug("PyDB enabled: exceptions will start a debugging session.")
except ImportError:
logging.warning("Could not import 'pydb' module - PyDB not enabled.")
if 'profile' in debug:
try:
import hotshot
pf = hotshot.Profile(__name__ + '.pf')
pf.start()
logging.debug("Started call profiling with 'hotshot' module.")
except ImportError:
logging.warning("Could not import 'hotshot' - call profiling *not* enabled.")
# hack to allow 'N1,N2,...' or 'N1 N2 ...' syntaxes
for (i, arg) in enumerate(cmdline.args):
if arg.find(","):
if arg.startswith('M'):
cmdline.args[i:i+1] = arg[1:].split(",")
else:
cmdline.args[i:i+1] = arg.split(",")
# open output file
if cmdline.outfile is None:
outfile = sys.stdout
else:
outfile = open(cmdline.outfile, 'w')
# shell -- start interactive debugging shell
if 'shell' == cmdline.action:
if cython_compiled:
logging.error("The 'shell' command is not available when compiled.")
sys.exit(1)
else:
try:
import pydb
except ImportError:
sys.stderr.write("ERROR: Could not import 'pydb' module - Aborting.\n")
logging.warning("Could not import 'pydb' module - Aborting.")
sys.exit(1)
print ("""Starting interactive session (with PyDB %s).
Any Python expression may be evaluated at the prompt.
All symbols from modules `rg`, `homology`, `graph_homology`
have already been imported into the main namespace.
""" % pydb.__version__)
pydb.debugger([
"from homology import *",
"from graph_homology import *",
"from rg import *",
])
# selftest -- run doctests and acceptance tests on simple cases
elif 'selftest' == cmdline.action:
failures = 0
import doctest
import imp
for module in [ 'rg',
'homology',
'graph_homology',
'combinatorics',
'iterators',
'cyclicseq',
]:
try:
module_file, pathname, description = imp.find_module(module, fatghol.__path__)
m = imp.load_module(module, module_file, pathname, description)
logging.debug("Running Python doctest on '%s' module..." % module)
# temporarily turn off logging to avoid cluttering the output
logging.getLogger().setLevel(logging.ERROR)
# run doctests
(failed, tested) = doctest.testmod(m, name=module, optionflags=doctest.NORMALIZE_WHITESPACE)
# restore normal logging level
logging.getLogger().setLevel(log_level)
if failed>0:
failures += 1
logging.error(" module '%s' FAILED %d tests out of %d." % (module, failed, tested))
sys.stdout.write("Module '%s' FAILED %d tests out of %d.\n" % (module, failed, tested))
else:
if tested>0:
logging.debug(" OK - module '%s' passed all doctests." % module)
sys.stdout.write("Module '%s' OK, passed all doctests.\n" % module)
else:
logging.warning(" module '%s' had no doctests." % module)
except Exception, ex:
try:
module_file.close()
except:
pass
raise ex
def run_homology_selftest(output=sys.stdout):
ok = True
# second, try known cases and inspect results
for (g, n, ok) in [ (0,3, [1,0,0]),
(0,4, [1,2,0,0,0,0]),
(0,5, [1,5,6,0,0,0,0,0,0]),
(1,1, [1,0,0]),
(1,2, [1,0,0,0,0,0]),
(2,1, [1,0,1,0,0,0,0,0,0]),
]:
output.write(" Computation of M_{%d,%d} homology: " % (g,n))
# compute homology of M_{g,n}
timing.start("homology M%d,%d" % (g,n))
hs = compute_homology(g,n)
timing.stop("homology M%d,%d" % (g,n))
# check result
if hs == ok:
output.write("OK (elapsed: %0.3fs)\n"
% timing.get("homology M%d,%d" % (g,n)))
else:
logging.error("Computation of M_{%d,%d} homology: FAILED, got %s expected %s"
% (g,n,hs,ok))
output.write("FAILED, got %s expected %s\n" % (hs,ok))
ok = False
return ok
## run the self-test suite 3 times:
##
## 1. without any persistence stuff enabled, so we can test the
## real results of the algorithm and the performance
sys.stdout.write("Checking homology algorithm (no checkpointing)\n")
try:
del runtime.options.checkpoint_dir
except AttributeError:
pass
ok = run_homology_selftest(sys.stdout)
if not ok:
failures += 1
## 2. run with a temporary checkpoint directory, to test saving of state
sys.stdout.write("Checking homology algorithm (checkpointing)\n")
runtime.options.checkpoint_dir = tempfile.mkdtemp(prefix="mgn.selftest.")
ok = run_homology_selftest(sys.stdout)
if not ok:
failures += 1
## 3. run with the same temporary directory, to test that
## persistence picks up results of rpevious runs correctly
sys.stdout.write("Checking homology algorithm (restoring from checkpointed state)\n")
ok = run_homology_selftest(sys.stdout)
if not ok:
failures += 1
# remove anything in the temporary directory
if failures == 0:
for entry in os.listdir(runtime.options.checkpoint_dir):
os.remove(os.path.join(runtime.options.checkpoint_dir, entry))
os.rmdir(runtime.options.checkpoint_dir)
else:
sys.stdout.write("Persisted files left in directory '%s'"
% runtime.options.checkpoint_dir)
# exit code >0 is number of failures
sys.exit(failures)
def run(args):
#atlas.relativeToOrigin = args.coordRelativeToOrigin
fileIn = None
coordT = None
niftiInput = None
# define data type for coordinates
if args.input_voxels:
ctype = int
query_voxel = True
else:
ctype = float
query_voxel = False
# Setup coordinates read-in
volQForm = None
#
# compatibility with older talairachlabel
if args.inputCoordFile:
fileIn = open(args.inputCoordFile)
coordsIterator = parsed_coordinates_iterator(
args.inputLineFormat, fileIn, ctype=ctype)
if args.inputVolFile:
infile = args.inputVolFile
# got a volume/file to process
if __debug__:
debug('ATL', "Testing if 0th element in the list a volume")
niftiInput = None
try:
niftiInput = nb.load(infile)
if __debug__:
debug('ATL', "Yes it is")
except Exception as e:
if __debug__:
debug('ATL', "No it is not due to %s. Trying to parse the file" % e)
if niftiInput:
# if we got here -- it is a proper volume
# XXX ask Michael to remove nasty warning message
coordsIterator = select_from_volume_iterator(
infile, args.lowerThreshold, args.upperThreshold)
assert(coordT is None)
coordT = Linear(niftiInput.header.get_qform())
# lets store volumeQForm for possible conversion of voxels into coordinates
volQForm = coordT
# previous iterator returns space coordinates
args.coordRelativeToOrigin = True
else:
raise ValueError('could not open volumetric input file')
# input is stdin
else:
coordsIterator = parsed_coordinates_iterator(
args.inputLineFormat, ctype=ctype)
# Open and initialize atlas lookup
if args.atlasFile is None:
if args.atlasPath is None:
args.atlasPath = KNOWN_ATLASES[args.atlasName]
args.atlasFile = args.atlasPath % ( {'name': args.atlasName} )
akwargs_common = {}
if args.atlasImageFile:
akwargs_common['image_file'] = args.atlasImageFile
if not args.forbidDirectMapping \
and niftiInput is not None and not args.transformationFile:
akwargs = {'resolution': niftiInput.header.get_zooms()[0]}
query_voxel = True # if we can query directly by voxel, do so
akwargs.update(akwargs_common)
verbose(1, "Will attempt direct mapping from input voxels into atlas "
"voxels at resolution %.2f" % akwargs['resolution'])
atlas = Atlas(args.atlasFile, **akwargs)
# verify that we got the same qforms in atlas and in the data file
if atlas.space != args.inputSpace:
verbose(0,
"Cannot do direct mapping between input image in %s space and"
" atlas in %s space. Use -I switch to override input space if"
" it misspecified, or use -T to provide transformation. Trying"
" to proceed" %(args.inputSpace, atlas.space))
query_voxel = False
elif not (niftiInput.header.get_qform() == atlas._image.header.get_qform()).all():
if args.atlasImageFile is None:
warning(
"Cannot do direct mapping between files with different qforms."
" Please provide original transformation (-T)."
"\n Input qform:\n%s\n Atlas qform: \n%s"
%(niftiInput.header.get_qform(), atlas._image.header.get_qform), 1)
# reset ability to query by voxels
query_voxel = False
else:
warning(
"QForms are different between input image and "
"provided atlas image."
"\n Input qform of %s:\n%s\n Atlas qform of %s:\n%s"
%(infile, niftiInput.header.get_qform(),
args.atlasImageFile, atlas._image.header.get_qform()), 1)
else:
coordT = None
else:
atlas = Atlas(args.atlasFile, **akwargs_common)
if isinstance(atlas, ReferencesAtlas):
args.referenceLevel = args.referenceLevel.replace('/', ' ')
atlas.set_reference_level(args.referenceLevel)
atlas.distance = args.maxDistance
else:
args.showReferencedCoordinates = False
if isinstance(atlas, FSLProbabilisticAtlas):
atlas.strategy = args.probStrategy
atlas.thr = args.probThr
## If not in Talairach -- in MNI with voxel size 2x2x2
# Original talairachlabel assumed that if respective to origin -- voxels were
# scaled already.
#if args.coordInTalairachSpace:
# voxelSizeOriginal = np.array([1, 1, 1])
#else:
# voxelSizeOriginal = np.array([2, 2, 2])
if args.coordInTalairachSpace:
args.inputSpace = "Talairach"
if not (args.inputSpace == atlas.space or
(args.inputSpace in ["MNI", "Talairach"] and
atlas.space == "Talairach")):
raise XMLAtlasException("Unknown space '%s' which is not the same as atlas "
"space '%s' either" % ( args.inputSpace, atlas.space ))
if query_voxel:
# we do direct mapping
coordT = None
else:
verbose(2, "Chaining needed transformations")
# by default -- no transformation
if args.transformationFile:
#externals.exists('scipy', raise_=True)
# scipy.io.read_array was deprecated a while back (around 0.8.0)
from numpy import loadtxt
transfMatrix = loadtxt(args.transformationFile)
coordT = Linear(transfMatrix, previous=coordT)
verbose(2, "coordT got linear transformation from file %s" %
args.transformationFile)
voxelOriginOriginal = None
voxelSizeOriginal = None
if not args.coordRelativeToOrigin:
if args.inputSpace == "Talairach":
# assume that atlas is in Talairach space already
voxelOriginOriginal = atlas.origin
voxelSizeOriginal = np.array([1, 1, 1])
elif args.inputSpace == "MNI":
# need to adjust for MNI origin as it was thought to be at
# in terms of voxels
#voxelOriginOriginal = np.array([46, 64, 37])
voxelOriginOriginal = np.array([45, 63, 36])
voxelSizeOriginal = np.array([2.0, 2.0, 2.0])
warning("Assuming elderly sizes for MNI volumes with"
" origin %s and sizes %s" %\
( repr(voxelOriginOriginal), repr(voxelSizeOriginal)))
if not (voxelOriginOriginal is None and voxelSizeOriginal is None):
verbose(2, "Assigning origin adjusting transformation with"+\
" origin=%s and voxelSize=%s" %\
( repr(voxelOriginOriginal), repr(voxelSizeOriginal)))
coordT = SpaceTransformation(origin=voxelOriginOriginal,
voxelSize=voxelSizeOriginal,
to_real_space=True, previous=coordT)
# besides adjusting for different origin we need to transform into
# Talairach space
if args.inputSpace == "MNI" and atlas.space == "Talairach":
verbose(2, "Assigning transformation %s" %
args.MNI2TalTransformation)
# What transformation to use
coordT = {"matthewbrett": MNI2Tal_MatthewBrett,
"lancaster07fsl": mni_to_tal_lancaster07_fsl,
"lancaster07pooled": mni_to_tal_lancaster07pooled,
"meyerlindenberg98": mni_to_tal_meyer_lindenberg98,
"yohflirt": mni_to_tal_yohflirt
}\
[args.MNI2TalTransformation](previous=coordT)
if args.inputSpace == "MNI" and args.halfVoxelCorrection:
originCorrection = np.array([0.5, 0.5, 0.5])
else:
# perform transformation any way to convert to voxel space (integers)
originCorrection = None
# To be closer to what original talairachlabel did -- add 0.5 to each coord
coordT = SpaceTransformation(origin=originCorrection, voxelSize=None,
to_real_space=False, previous = coordT)
if args.createSummary:
summary = {}
if args.levels is None:
args.levels = str(min(4, atlas.nlevels-1))
if args.levels is None:
args.levels = list(range(atlas.nlevels))
elif isinstance(args.levels, str):
if args.levels == 'list':
print("Known levels and their indicies:\n" + atlas.levels_listing())
sys.exit(0)
slevels = args.levels.split(',')
args.levels = []
for level in slevels:
try:
int_level = int(level)
except:
if level in atlas.levels:
int_level = atlas.levels[level].index
else:
raise RuntimeError(
"Unknown level '%s'. " % level +
"Known levels and their indicies:\n"
+ atlas.levels_listing())
args.levels += [int_level]
else:
raise ValueError("Don't know how to handle list of levels %s."
"Example is '1,2,3'" % (args.levels,))
verbose(3, "Operating on following levels: %s" % args.levels)
# assign levels to the atlas
atlas.default_levels = args.levels
if args.outputFile:
output = open(args.outputFile, 'w')
else:
output = sys.stdout
# validity check
if args.dumpmapFile:
if niftiInput is None:
raise RuntimeError("You asked to dump indexes into the volume, " \
"but input wasn't a volume")
sys.exit(1)
ni_dump = nb.load(infile)
ni_dump_data = np.zeros(ni_dump.header.get_data_shape()[:3] + (len(args.levels),))
# Also check if we have provided voxels but not querying by voxels
if args.input_voxels:
if coordT is not None:
raise NotImplementedError("Cannot perform voxels querying having coordT defined")
if not query_voxel:
raise NotImplementedError("query_voxel was reset to False, can't do queries by voxel")
# Read coordinates
numVoxels = 0
for c in coordsIterator:
value, coord_orig, t = c[0], c[1:4], c[4]
if __debug__:
debug('ATL', "Obtained coord_orig=%s with value %s"
% (repr(coord_orig), value))
lt, ut = args.lowerThreshold, args.upperThreshold
if lt is not None and value < lt:
verbose(5, "Value %s is less than lower threshold %s, thus voxel "
"is skipped" % (value, args.lowerThreshold))
continue
if ut is not None and value > ut:
verbose(5, "Value %s is greater than upper threshold %s, thus voxel "
"is skipped" % (value, args.upperThreshold))
continue
numVoxels += 1
# Apply necessary transformations
coord = coord_orig = np.array(coord_orig)
if coordT:
coord = coordT[ coord_orig ]
# Query label
if query_voxel:
voxel = atlas[coord]
else:
voxel = atlas(coord)
voxel['coord_orig'] = coord_orig
voxel['value'] = value
voxel['t'] = t
if args.createSummary:
summaryIndex = ""
voxel_labels = voxel["labels"]
for i,ind in enumerate(args.levels):
voxel_label = voxel_labels[i]
text = present_labels(args, voxel_label)
#if len(voxel_label):
# assert(voxel_label['index'] == ind)
summaryIndex += text + " / "
if not summaryIndex in summary:
summary[summaryIndex] = {'values':[], 'max':value,
'maxcoord':coord_orig}
if 'voxel_referenced' in voxel:
summary[summaryIndex]['distances'] = []
summary_ = summary[summaryIndex]
summary_['values'].append(value)
if summary_['max'] < value:
summary_['max'] = value
summary_['maxcoord'] = coord_orig
if 'voxel_referenced' in voxel:
if voxel['voxel_referenced'] and voxel['distance']>=1e-3:
verbose(5, 'Appending distance %e for voxel at %s'
% (voxel['distance'], voxel['coord_orig']))
summary_['distances'].append(voxel['distance'])
else:
# Display while reading/processing
first, out = True, ""
if args.showValues:
out += "%(value)5.2f "
if args.showOriginalCoordinates:
out += "%(coord_orig)s ->"
if args.showReferencedCoordinates:
out += " %(voxel_referenced)s=>%(distance).2f=>%(voxel_queried)s ->"
if args.showTargetCoordinates:
out += " %(coord_queried)s: "
#out += "(%d,%d,%d): " % tuple(map(lambda x:int(round(x)),coord))
if args.showTargetVoxel:
out += " %(voxel_queried)s ->"
if args.levels is None:
args.levels = list(range(len(voxel['labels'])))
labels = [present_labels(args, voxel['labels'][i]) for i in args.levels]
out += ','.join(labels)
#if args.abbreviatedLabels:
# out += ','.join([l.abbr for l in labels])
#else:
# out += ','.join([l.text for l in labels])
#try:
output.write(out % voxel + "\n")
#except:
# import pydb
# pydb.debugger()
if args.dumpmapFile:
try:
ni_dump_data[coord_orig[0], coord_orig[1], coord_orig[2]] = \
[voxel['labels'][i]['label'].index
for i,ind in enumerate(args.levels)]
except Exception as e:
import pydb
pydb.debugger()
# if we opened any file -- close it
if fileIn:
fileIn.close()
if args.dumpmapFile:
ni_dump = nb.Nifti1Image(ni_dump_data, None, ni_dump.header)
ni_dump.to_filename(args.dumpmapFile)
if args.createSummary:
if numVoxels == 0:
verbose(1, "No matching voxels were found.")
else:
get_summary(args, summary, output)
if args.outputFile:
output.close()
#!/usr/bin/python
"""Towers of Hanoi - testing calling debugger with continue and cmds"""
import sys
sys.path.insert(0, '..')
import pydb
pydb.debugger(dbg_cmds=['set basename on', 'set linetrace on', 'step 20'])
def hanoi(n,a,b,c):
if n-1 > 0:
hanoi(n-1, a, c, b)
print "Move disk %s to %s" % (a, b)
if n-1 > 0:
hanoi(n-1, c, b, a)
if __name__=='__main__':
i_args=len(sys.argv)
if i_args != 1 and i_args != 2:
print "*** Need number of disks or no parameter"
sys.exit(1)
n=3
sys.settrace(None)
if i_args > 1:
try:
n = int(sys.argv[1])
except ValueError, msg:
print "** Expecting an integer, got: %s" % repr(sys.argv[1])
sys.exit(2)