def load_config_yml(config_file, individual=False):
# loads a configuration YAML file
#
# input
# config_file: full filepath to YAML (.yml) file
#
# output
# config: Configuration object
import os
import yaml
from CPAC.utils import Configuration
try:
config_path = os.path.realpath(config_file)
with open(config_path, "r") as f:
config_dict = yaml.load(f)
config = Configuration(config_dict)
except Exception as e:
err = "\n\n[!] CPAC says: Could not load or read the configuration " \
"YAML file:\n%s\nDetails: %s\n\n" % (config_file, e)
raise Exception(err)
if individual:
config.logDirectory = os.path.abspath(config.logDirectory)
config.workingDirectory = os.path.abspath(config.workingDirectory)
config.outputDirectory = os.path.abspath(config.outputDirectory)
config.crashLogDirectory = os.path.abspath(config.crashLogDirectory)
return config
def run(config_file, subject_list_file, p_name=None, plugin=None,
plugin_args=None, tracking=True, num_subs_at_once=None, debug=False):
'''
'''
# Import packages
import commands
import os
import pickle
import time
from CPAC.pipeline.cpac_pipeline import prep_workflow
# Init variables
config_file = os.path.realpath(config_file)
subject_list_file = os.path.realpath(subject_list_file)
# take date+time stamp for run identification purposes
unique_pipeline_id = strftime("%Y%m%d%H%M%S")
pipeline_start_stamp = strftime("%Y-%m-%d_%H:%M:%S")
# Load in pipeline config file
try:
if not os.path.exists(config_file):
raise IOError
else:
c = Configuration(yaml.load(open(config_file, 'r')))
except IOError:
print "config file %s doesn't exist" % config_file
raise
except Exception as e:
raise Exception("Error reading config file - {0}\n\nError details:"
"\n{1}\n\n".format(config_file, e))
c.logDirectory = os.path.abspath(c.logDirectory)
c.workingDirectory = os.path.abspath(c.workingDirectory)
if 's3://' not in c.outputDirectory:
c.outputDirectory = os.path.abspath(c.outputDirectory)
c.crashLogDirectory = os.path.abspath(c.crashLogDirectory)
if debug:
c.write_debugging_outputs = "[1]"
if num_subs_at_once:
if not str(num_subs_at_once).isdigit():
raise Exception('[!] Value entered for --num_cores not a digit.')
c.numParticipantsAtOnce = int(num_subs_at_once)
# Do some validation
validate(c)
# Get the pipeline name
p_name = p_name or c.pipelineName
# Load in subject list
try:
with open(subject_list_file, 'r') as sf:
sublist = yaml.load(sf)
except:
print "Subject list is not in proper YAML format. Please check " \
"your file"
raise Exception
# Populate subject scan map
sub_scan_map = {}
try:
for sub in sublist:
if sub['unique_id']:
s = sub['subject_id'] + "_" + sub["unique_id"]
else:
s = sub['subject_id']
scan_ids = ['scan_anat']
if 'func' in sub:
for id in sub['func']:
scan_ids.append('scan_'+ str(id))
if 'rest' in sub:
for id in sub['rest']:
scan_ids.append('scan_'+ str(id))
sub_scan_map[s] = scan_ids
except:
print "\n\n" + "ERROR: Subject list file not in proper format - " \
"check if you loaded the correct file?" + "\n" + \
"Error name: cpac_runner_0001" + "\n\n"
raise Exception
pipeline_timing_info = []
pipeline_timing_info.append(unique_pipeline_id)
pipeline_timing_info.append(pipeline_start_stamp)
pipeline_timing_info.append(len(sublist))
if tracking:
track_run(level='participant', participants=len(sublist))
# If we're running on cluster, execute job scheduler
if c.runOnGrid:
# Create cluster log dir
cluster_files_dir = os.path.join(c.logDirectory, 'cluster_files')
if not os.path.exists(cluster_files_dir):
os.makedirs(cluster_files_dir)
# Check if its a condor job, and run that
if 'condor' in c.resourceManager.lower():
run_condor_jobs(c, config_file, subject_list_file, p_name)
# All other schedulers are supported
else:
run_cpac_on_cluster(config_file, subject_list_file, cluster_files_dir)
# Run on one computer
else:
if not os.path.exists(c.workingDirectory):
try:
os.makedirs(c.workingDirectory)
except:
err = "\n\n[!] CPAC says: Could not create the working " \
"directory: %s\n\nMake sure you have permissions " \
"to write to this directory.\n\n" % c.workingDirectory
raise Exception(err)
# If it only allows one, run it linearly
if c.numParticipantsAtOnce == 1:
for sub in sublist:
prep_workflow(sub, c, True, pipeline_timing_info,
p_name, plugin, plugin_args)
return
pid = open(os.path.join(c.workingDirectory, 'pid.txt'), 'w')
# Init job queue
job_queue = []
# Allocate processes
processes = [Process(target=prep_workflow,
args=(sub, c, True, pipeline_timing_info,
p_name, plugin, plugin_args))
for sub in sublist]
# If we're allocating more processes than are subjects, run them all
if len(sublist) <= c.numParticipantsAtOnce:
for p in processes:
p.start()
print >>pid, p.pid
# Otherwise manage resources to run processes incrementally
else:
idx = 0
while idx < len(sublist):
# If the job queue is empty and we haven't started indexing
if len(job_queue) == 0 and idx == 0:
# Init subject process index
idc = idx
# Launch processes (one for each subject)
for p in processes[idc: idc+c.numParticipantsAtOnce]:
p.start()
print >>pid, p.pid
job_queue.append(p)
idx += 1
# Otherwise, jobs are running - check them
else:
# Check every job in the queue's status
for job in job_queue:
# If the job is not alive
if not job.is_alive():
# Find job and delete it from queue
print 'found dead job ', job
loc = job_queue.index(job)
del job_queue[loc]
# ...and start the next available process
# (subject)
processes[idx].start()
# Append this to job queue and increment index
job_queue.append(processes[idx])
idx += 1
# Add sleep so while loop isn't consuming 100% of CPU
time.sleep(2)
# Close PID txt file to indicate finish
pid.close()
def run(config_file,
subject_list_file,
p_name=None,
plugin=None,
plugin_args=None,
tracking=True,
num_subs_at_once=None):
'''
'''
# Import packages
import commands
import os
import pickle
import time
from CPAC.pipeline.cpac_pipeline import prep_workflow
# Init variables
config_file = os.path.realpath(config_file)
subject_list_file = os.path.realpath(subject_list_file)
# take date+time stamp for run identification purposes
unique_pipeline_id = strftime("%Y%m%d%H%M%S")
pipeline_start_stamp = strftime("%Y-%m-%d_%H:%M:%S")
# Load in pipeline config file
try:
if not os.path.exists(config_file):
raise IOError
else:
c = Configuration(yaml.load(open(config_file, 'r')))
except IOError:
print "config file %s doesn't exist" % config_file
raise
except Exception as e:
raise Exception("Error reading config file - {0}\n\nError details:"
"\n{1}\n\n".format(config_file, e))
c.logDirectory = os.path.abspath(c.logDirectory)
c.workingDirectory = os.path.abspath(c.workingDirectory)
c.outputDirectory = os.path.abspath(c.outputDirectory)
c.crashLogDirectory = os.path.abspath(c.crashLogDirectory)
if num_subs_at_once:
if not str(num_subs_at_once).isdigit():
raise Exception('[!] Value entered for --num_cores not a digit.')
c.numParticipantsAtOnce = int(num_subs_at_once)
# Do some validation
validate(c)
# Get the pipeline name
p_name = p_name or c.pipelineName
# Load in subject list
try:
with open(subject_list_file, 'r') as sf:
sublist = yaml.load(sf)
except:
print "Subject list is not in proper YAML format. Please check " \
"your file"
raise Exception
# NOTE: strategies list is only needed in cpac_pipeline prep_workflow for
# creating symlinks
strategies = sorted(build_strategies(c))
# Populate subject scan map
sub_scan_map = {}
try:
for sub in sublist:
if sub['unique_id']:
s = sub['subject_id'] + "_" + sub["unique_id"]
else:
s = sub['subject_id']
scan_ids = ['scan_anat']
if 'func' in sub:
for id in sub['func']:
scan_ids.append('scan_' + str(id))
if 'rest' in sub:
for id in sub['rest']:
scan_ids.append('scan_' + str(id))
sub_scan_map[s] = scan_ids
except:
print "\n\n" + "ERROR: Subject list file not in proper format - " \
"check if you loaded the correct file?" + "\n" + \
"Error name: cpac_runner_0001" + "\n\n"
raise Exception
pipeline_timing_info = []
pipeline_timing_info.append(unique_pipeline_id)
pipeline_timing_info.append(pipeline_start_stamp)
pipeline_timing_info.append(len(sublist))
if tracking:
track_run(level='participant', participants=len(sublist))
# If we're running on cluster, execute job scheduler
if c.runOnGrid:
# Create cluster log dir
cluster_files_dir = os.path.join(c.logDirectory, 'cluster_files')
if not os.path.exists(cluster_files_dir):
os.makedirs(cluster_files_dir)
# Create strategies file
strategies_file = os.path.join(cluster_files_dir, 'strategies.pkl')
with open(strategies_file, 'w') as f:
pickle.dump(strategies, f)
# Check if its a condor job, and run that
if 'condor' in c.resourceManager.lower():
run_condor_jobs(c, config_file, strategies_file, subject_list_file,
p_name)
# All other schedulers are supported
else:
run_cpac_on_cluster(config_file, subject_list_file,
strategies_file, cluster_files_dir)
# Run on one computer
else:
if not os.path.exists(c.workingDirectory):
try:
os.makedirs(c.workingDirectory)
except:
err = "\n\n[!] CPAC says: Could not create the working " \
"directory: %s\n\nMake sure you have permissions " \
"to write to this directory.\n\n" % c.workingDirectory
raise Exception(err)
# If it only allows one, run it linearly
if c.numParticipantsAtOnce == 1:
for sub in sublist:
prep_workflow(sub, c, strategies, 1, pipeline_timing_info,
p_name, plugin, plugin_args)
return
pid = open(os.path.join(c.workingDirectory, 'pid.txt'), 'w')
# Init job queue
job_queue = []
# Allocate processes
processes = [
Process(target=prep_workflow,
args=(sub, c, strategies, 1, pipeline_timing_info, p_name,
plugin, plugin_args)) for sub in sublist
]
# If we're allocating more processes than are subjects, run them all
if len(sublist) <= c.numParticipantsAtOnce:
for p in processes:
p.start()
print >> pid, p.pid
# Otherwise manage resources to run processes incrementally
else:
idx = 0
while idx < len(sublist):
# If the job queue is empty and we haven't started indexing
if len(job_queue) == 0 and idx == 0:
# Init subject process index
idc = idx
# Launch processes (one for each subject)
for p in processes[idc:idc + c.numParticipantsAtOnce]:
p.start()
print >> pid, p.pid
job_queue.append(p)
idx += 1
# Otherwise, jobs are running - check them
else:
# Check every job in the queue's status
for job in job_queue:
# If the job is not alive
if not job.is_alive():
# Find job and delete it from queue
print 'found dead job ', job
loc = job_queue.index(job)
del job_queue[loc]
# ...and start the next available process
# (subject)
processes[idx].start()
# Append this to job queue and increment index
job_queue.append(processes[idx])
idx += 1
# Add sleep so while loop isn't consuming 100% of CPU
time.sleep(2)
# Close PID txt file to indicate finish
pid.close()
def run(subject_list_file, config_file=None, p_name=None, plugin=None,
plugin_args=None, tracking=True, num_subs_at_once=None, debug=False, test_config=False):
# Import packages
import commands
import os
import pickle
import time
from CPAC.pipeline.cpac_pipeline import prep_workflow
print('Run called with config file {0}'.format(config_file))
if not config_file:
import pkg_resources as p
config_file = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"pipeline_config_template.yml"))
# Init variables
sublist = None
config_file = os.path.realpath(config_file)
if '.yaml' in subject_list_file or '.yml' in subject_list_file:
subject_list_file = os.path.realpath(subject_list_file)
else:
from CPAC.utils.bids_utils import collect_bids_files_configs, \
bids_gen_cpac_sublist
(file_paths, config) = collect_bids_files_configs(subject_list_file,
None)
sublist = bids_gen_cpac_sublist(subject_list_file, file_paths,
config, None)
if not sublist:
import sys
print("Did not find data in {0}".format(subject_list_file))
sys.exit(1)
# take date+time stamp for run identification purposes
unique_pipeline_id = strftime("%Y%m%d%H%M%S")
pipeline_start_stamp = strftime("%Y-%m-%d_%H:%M:%S")
# Load in pipeline config file
try:
if not os.path.exists(config_file):
raise IOError
else:
c = Configuration(yaml.load(open(config_file, 'r')))
except IOError:
print "config file %s doesn't exist" % config_file
raise
except yaml.parser.ParserError as e:
error_detail = "\"%s\" at line %d" % (
e.problem,
e.problem_mark.line
)
raise Exception(
"Error parsing config file: {0}\n\n"
"Error details:\n"
" {1}"
"\n\n".format(config_file, error_detail)
)
except Exception as e:
raise Exception(
"Error parsing config file: {0}\n\n"
"Error details:\n"
" {1}"
"\n\n".format(config_file, e)
)
c.logDirectory = os.path.abspath(c.logDirectory)
c.workingDirectory = os.path.abspath(c.workingDirectory)
if 's3://' not in c.outputDirectory:
c.outputDirectory = os.path.abspath(c.outputDirectory)
c.crashLogDirectory = os.path.abspath(c.crashLogDirectory)
if debug:
c.write_debugging_outputs = "[1]"
if num_subs_at_once:
if not str(num_subs_at_once).isdigit():
raise Exception('[!] Value entered for --num_cores not a digit.')
c.numParticipantsAtOnce = int(num_subs_at_once)
# Do some validation
if not c.workingDirectory:
raise Exception('Working directory not specified')
if len(c.workingDirectory) > 70:
warnings.warn("We recommend that the working directory full path "
"should have less then 70 characters. "
"Long paths might not work in your operational system.")
warnings.warn("Current working directory: %s" % c.workingDirectory)
# Get the pipeline name
p_name = p_name or c.pipelineName
# Load in subject list
try:
if not sublist:
with open(subject_list_file, 'r') as sf:
sublist = yaml.load(sf)
except:
print "Subject list is not in proper YAML format. Please check " \
"your file"
raise Exception
# Populate subject scan map
sub_scan_map = {}
try:
for sub in sublist:
if sub['unique_id']:
s = sub['subject_id'] + "_" + sub["unique_id"]
else:
s = sub['subject_id']
scan_ids = ['scan_anat']
if 'func' in sub:
for id in sub['func']:
scan_ids.append('scan_'+ str(id))
if 'rest' in sub:
for id in sub['rest']:
scan_ids.append('scan_'+ str(id))
sub_scan_map[s] = scan_ids
except:
print "\n\n" + "ERROR: Subject list file not in proper format - " \
"check if you loaded the correct file?" + "\n" + \
"Error name: cpac_runner_0001" + "\n\n"
raise Exception
pipeline_timing_info = []
pipeline_timing_info.append(unique_pipeline_id)
pipeline_timing_info.append(pipeline_start_stamp)
pipeline_timing_info.append(len(sublist))
if tracking:
try:
track_run(level='participant', participants=len(sublist))
except:
pass
# If we're running on cluster, execute job scheduler
if c.runOnGrid:
# Create cluster log dir
cluster_files_dir = os.path.join(c.logDirectory, 'cluster_files')
if not os.path.exists(cluster_files_dir):
os.makedirs(cluster_files_dir)
# Check if its a condor job, and run that
if 'condor' in c.resourceManager.lower():
run_condor_jobs(c, config_file, subject_list_file, p_name)
# All other schedulers are supported
else:
run_cpac_on_cluster(config_file, subject_list_file, cluster_files_dir)
# Run on one computer
else:
if not os.path.exists(c.workingDirectory):
try:
os.makedirs(c.workingDirectory)
except:
err = "\n\n[!] CPAC says: Could not create the working " \
"directory: %s\n\nMake sure you have permissions " \
"to write to this directory.\n\n" % c.workingDirectory
raise Exception(err)
# If it only allows one, run it linearly
if c.numParticipantsAtOnce == 1:
for sub in sublist:
prep_workflow(sub, c, True, pipeline_timing_info,
p_name, plugin, plugin_args, test_config)
return
pid = open(os.path.join(c.workingDirectory, 'pid.txt'), 'w')
# Init job queue
job_queue = []
# Allocate processes
processes = [
Process(target=prep_workflow,
args=(sub, c, True, pipeline_timing_info,
p_name, plugin, plugin_args, test_config))
for sub in sublist
]
# If we're allocating more processes than are subjects, run them all
if len(sublist) <= c.numParticipantsAtOnce:
for p in processes:
p.start()
print >>pid, p.pid
# Otherwise manage resources to run processes incrementally
else:
idx = 0
while idx < len(sublist):
# If the job queue is empty and we haven't started indexing
if len(job_queue) == 0 and idx == 0:
# Init subject process index
idc = idx
# Launch processes (one for each subject)
for p in processes[idc: idc+c.numParticipantsAtOnce]:
p.start()
print >>pid, p.pid
job_queue.append(p)
idx += 1
# Otherwise, jobs are running - check them
else:
# Check every job in the queue's status
for job in job_queue:
# If the job is not alive
if not job.is_alive():
# Find job and delete it from queue
print 'found dead job ', job
loc = job_queue.index(job)
del job_queue[loc]
# ...and start the next available process
# (subject)
processes[idx].start()
# Append this to job queue and increment index
job_queue.append(processes[idx])
idx += 1
# Add sleep so while loop isn't consuming 100% of CPU
time.sleep(2)
# Close PID txt file to indicate finish
pid.close()