def display_crash_files(crashfile, rerun=False):
from nipype.utils.filemanip import loadcrash
crash_data = loadcrash(crashfile)
node = crash_data['node']
tb = crash_data['traceback']
print("\n")
print("File: %s"%crashfile)
print("Node: %s"%node)
if node.base_dir:
print("Working directory: %s" % node.output_dir())
else:
print("Node crashed before execution")
print("\n")
print("Node inputs:")
print(node.inputs)
print("\n")
print("Traceback: ")
print(''.join(tb))
print("\n")
if rerun:
print("Rerunning node")
node.base_dir = None
node.config['crashdump_dir'] = '/tmp'
node.run()
print("\n")
def read_crash(path, touch_dir=None):
try:
crash_report = '\n'.join(loadcrash(path).get('traceback', []))
print(crash_report)
except TraitError as e:
touched_dir = _touch_trait_error_path(e.args[0])
if (touch_dir and touched_dir != touch_dir) or (not touch_dir):
# Disallow repeated attempts to touch the same file
read_crash(path, touched_dir)
def load_pklz_traceback(crash_filepath):
"""Return the traceback message in the given crash file."""
try:
data = loadcrash(crash_filepath)
except TraitError as te:
return str(te)
except:
raise
else:
return "\n".join(data["traceback"])
def load_pklz_traceback(crash_filepath):
"""Return the traceback message in the given crash file."""
try:
data = loadcrash(crash_filepath)
except TraitError as te:
return str(te)
except:
raise
else:
return '\n'.join(data['traceback'])
def _read_pkl(path):
from nipype.utils.filemanip import loadcrash
crash_data = loadcrash(path)
data = {'file': path, 'traceback': ''.join(crash_data['traceback'])}
if 'node' in crash_data:
data['node'] = crash_data['node']
if data['node'].base_dir:
data['node_dir'] = data['node'].output_dir()
else:
data['node_dir'] = "Node crashed before execution"
data['inputs'] = sorted(data['node'].inputs.trait_get().items())
return data
def _read_pkl(fname):
crash_data = loadcrash(fname)
data = {'file': fname,
'traceback': ''.join(crash_data['traceback']).replace("\\n", "<br \>")}
if 'node' in crash_data:
data['node'] = crash_data['node']
if data['node'].base_dir:
data['node_dir'] = data['node'].output_dir()
else:
data['node_dir'] = "Node crashed before execution"
data['inputs'] = sorted(data['node'].inputs.trait_get().items())
return data
def _read_pkl(path):
from nipype.utils.filemanip import loadcrash
crash_data = loadcrash(path)
data = {"file": path, "traceback": "".join(crash_data["traceback"])}
if "node" in crash_data:
data["node"] = crash_data["node"]
if data["node"].base_dir:
data["node_dir"] = data["node"].output_dir()
else:
data["node_dir"] = "Node crashed before execution"
data["inputs"] = sorted(data["node"].inputs.trait_get().items())
return data
def display_crash_file(crashfile, rerun, debug, directory):
"""display crash file content and rerun if required"""
from nipype.utils.filemanip import loadcrash
crash_data = loadcrash(crashfile)
node = None
if "node" in crash_data:
node = crash_data["node"]
tb = crash_data["traceback"]
print("\n")
print("File: %s" % crashfile)
if node:
print("Node: %s" % node)
if node.base_dir:
print("Working directory: %s" % node.output_dir())
else:
print("Node crashed before execution")
print("\n")
print("Node inputs:")
print(node.inputs)
print("\n")
print("Traceback: ")
print("".join(tb))
print("\n")
if rerun:
if node is None:
print("No node in crashfile. Cannot rerun")
return
print("Rerunning node")
node.base_dir = directory
node.config = {"execution": {"crashdump_dir": "/tmp"}}
try:
node.run()
except:
if debug and debug != "ipython":
import pdb
pdb.post_mortem()
else:
raise
print("\n")
def display_crash_file(crashfile, rerun, debug, directory):
"""display crash file content and rerun if required"""
from nipype.utils.filemanip import loadcrash
crash_data = loadcrash(crashfile)
node = None
if 'node' in crash_data:
node = crash_data['node']
tb = crash_data['traceback']
print("\n")
print("File: %s" % crashfile)
if node:
print("Node: %s" % node)
if node.base_dir:
print("Working directory: %s" % node.output_dir())
else:
print("Node crashed before execution")
print("\n")
print("Node inputs:")
print(node.inputs)
print("\n")
print("Traceback: ")
print(''.join(tb))
print("\n")
if rerun:
if node is None:
print("No node in crashfile. Cannot rerun")
return
print("Rerunning node")
node.base_dir = directory
node.config = {'execution': {'crashdump_dir': '/tmp'}}
try:
node.run()
except:
if debug and debug != 'ipython':
import pdb
pdb.post_mortem()
else:
raise
print("\n")
def index_error_dir(self, error_dir):
''' Crawl subjects crash directory for the corresponding run and return text for
.pklz crash file found. '''
for root, directories, filenames in os.walk(error_dir):
for f in filenames:
# Only deal with files that start with crash and end in pklz
if not (f[:5] == 'crash' and f[-4:] == 'pklz'):
continue
crash_data = loadcrash(os.path.join(root, f))
error = {}
node = None
if 'node' in crash_data:
node = crash_data['node']
error['traceback'] = ''.join(crash_data['traceback']).replace("\\n", "<br \>")
error['file'] = f
if node:
error['node'] = node
if node.base_dir:
error['node_dir'] = node.output_dir()
else:
error['node_dir'] = "Node crashed before execution"
error['inputs'] = sorted(node.inputs.trait_get().items())
self.errors.append(error)
def generate_xml_nodes(sourceDir,targetDir,pvc_method,tka_method):
listOfNodes = [
{"name" : "pet2mri",
"mnc_inputs" : {"node" : "pet2mri", "file" : 'in_target_file'},
"mnc_outputs" : {"node" : "pet2mri", "file" : 'out_file_img'}
}];
if pvc_method != None :
listOfNodes.append({"name" : "pvc",
"mnc_inputs" : {"node" : pvc_method, "file" : 'in_file'},
"mnc_outputs" : {"node" : pvc_method, "file" : 'out_file'}
});
if tka_method != None :
listOfNodes.append({"name" : "tka",
"mnc_inputs" : {"node" : "convertParametric", "file" : 'out_file'},
"mnc_outputs" : {"node" : "pet2mri", "file" : 'in_target_file'}
});
filename=targetDir+"/preproc/graph1.json";
fp = file(filename, 'r')
data=json.load(fp)
fp.close()
xmlQC = Element('qc')
listVolumes = list();
for subjIdx in range(0,len(data["groups"])):
for nodeID in range(data["groups"][subjIdx]["procs"][0],data["groups"][subjIdx]["procs"][-1]):
nodeName = "_".join(data["nodes"][nodeID]["name"].split("_")[1:])
if nodeName == "datasourcePET":
nodeReport = loadcrash(targetDir+"/preproc/"+data["nodes"][nodeID]["result"])
for key, value in nodeReport.inputs.items():
if key == "cid":
cid = str(value)
if key == "sid":
sid = str(value)
xmlscan = SubElement(xmlQC, 'scan')
xmlscan.set('sid', sid)
xmlscan.set('cid', cid)
for x in listOfNodes :
xmlnode = SubElement(xmlscan, 'node')
xmlnode.set('name', x['name'])
for nodeID in range(data["groups"][subjIdx]["procs"][0],data["groups"][subjIdx]["procs"][-1]):
nodeName = "_".join(data["nodes"][nodeID]["name"].split("_")[1:])
if nodeName == x["mnc_inputs"]["node"]:
nodeReport = loadcrash(targetDir+"/preproc/"+data["nodes"][nodeID]["result"])
xmlmnc = SubElement(xmlnode, 'inMnc')
for key, value in nodeReport.inputs.items():
if key in x['mnc_inputs']["file"]:
value = value[0] if type(value) == list else value
xmlkey = SubElement(xmlmnc, str(key))
xmlkey.text = str(value).replace(sourceDir+"/",'').replace(targetDir+"/",'')
listVolumes.append(str(value))
if nodeName == x["mnc_outputs"]["node"]:
nodeReport = loadcrash(targetDir+"/preproc/"+data["nodes"][nodeID]["result"])
xmlmnc = SubElement(xmlnode, 'outMnc')
for key, value in nodeReport.inputs.items():
if key in x['mnc_outputs']["file"]:
value = value[0] if type(value) == list else value
xmlkey = SubElement(xmlmnc, str(key))
xmlkey.text = str(value).replace(sourceDir+"/",'').replace(targetDir+"/",'')
listVolumes.append(str(value))
with open(targetDir+"/preproc/dashboard/public/nodes.xml","w") as f:
f.write(prettify(xmlQC))
for mincfile in listVolumes:
rawfile = mincfile+'.raw'
headerfile = mincfile+'.header'
if not os.path.exists(rawfile) or not os.path.exists(headerfile):
adjust_hdr(mincfile)
mnc2vol(mincfile)
