def output_hdul(set_inandout_filenames, config):
set_inandout_filenames_info = core_utils.read_info4outputhdul(config, set_inandout_filenames)
step, txt_name, step_input_file, step_output_file, run_calwebb_spec2, outstep_file_suffix = set_inandout_filenames_info
skip_runing_pipe_step = config.getboolean("tests_only", "_".join((step, "tests")))
# Only run step if data is not IFU
inhdu = core_utils.read_hdrfits(step_input_file, info=False, show_hdr=False)
end_time = '0.0'
print("Is the input file IFU? = ", core_utils.check_IFU_true(inhdu))
if not core_utils.check_IFU_true(inhdu):
stp = ResampleSpecStep()
# if run_calwebb_spec2 is True calwebb_spec2 will be called, else individual steps will be ran
step_completed = False
if run_calwebb_spec2:
# read the assign wcs fits file
local_step_output_file = core_utils.read_completion_to_full_run_map("full_run_map.txt", step)
hdul = core_utils.read_hdrfits(local_step_output_file, info=False, show_hdr=False)
# move the output file into the working directory
working_directory = config.get("calwebb_spec2_input_file", "working_directory")
step_output_file = os.path.join(working_directory, local_step_output_file)
print ("Step product was saved as: ", step_output_file)
subprocess.run(["mv", local_step_output_file, step_output_file])
return hdul
else:
if config.getboolean("steps", step):
print ("*** Step "+step+" set to True")
if os.path.isfile(step_input_file):
if not skip_runing_pipe_step:
# get the right configuration files to run the step
local_pipe_cfg_path = config.get("calwebb_spec2_input_file", "local_pipe_cfg_path")
# start the timer to compute the step running time
start_time = time.time()
if local_pipe_cfg_path == "pipe_source_tree_code":
result = stp.call(step_input_file)
else:
result = stp.call(step_input_file, config_file=local_pipe_cfg_path+'/resample_spec.cfg')
result.save(step_output_file)
# end the timer to compute the step running time
end_time = repr(time.time() - start_time) # this is in seconds
print("Step "+step+" took "+end_time+" seconds to finish")
step_completed = True
core_utils.add_completed_steps(txt_name, step, outstep_file_suffix, step_completed, end_time)
hdul = core_utils.read_hdrfits(step_output_file, info=False, show_hdr=False)
return hdul
else:
core_utils.add_completed_steps(txt_name, step, outstep_file_suffix, step_completed, end_time)
pytest.skip("Skipping "+step+" because the input file does not exist.")
else:
core_utils.add_completed_steps(txt_name, step, outstep_file_suffix, step_completed, end_time)
pytest.skip("Skipping "+step+". Step set to False in configuration file.")
else:
pytest.skip("Skipping "+step+" because data is IFU data and the resample will be done in cube_build.")
def output_hdul(set_inandout_filenames, config):
set_inandout_filenames_info = core_utils.read_info4outputhdul(
config, set_inandout_filenames)
step, txt_name, step_input_file, step_output_file, run_calwebb_spec2, outstep_file_suffix = set_inandout_filenames_info
run_pipe_step = config.getboolean("run_pipe_steps", step)
# determine which tests are to be run
resample_spec_completion_tests = config.getboolean(
"run_pytest", "_".join((step, "completion", "tests")))
#resample_spec_reffile_tests = config.getboolean("run_pytest", "_".join((step, "reffile", "tests")))
#resample_spec_validation_tests = config.getboolean("run_pytest", "_".join((step, "validation", "tests")))
run_pytests = [
resample_spec_completion_tests
] #, resample_spec_reffile_tests, resample_spec_validation_tests]
end_time = '0.0'
# Only run step if data is not IFU or BOTS
mode_used = config.get("calwebb_spec2_input_file", "mode_used").lower()
working_directory = config.get("calwebb_spec2_input_file",
"working_directory")
initial_input_file = config.get("calwebb_spec2_input_file", "input_file")
initial_input_file = os.path.join(working_directory, initial_input_file)
detector = fits.getval(initial_input_file, "DETECTOR", 0)
if not os.path.isfile(initial_input_file):
pytest.skip(
"Skipping " + step +
" because the initial input file given in PTT_config.cfg does not exist."
)
if mode_used != "bots" and mode_used != "ifu":
# if run_calwebb_spec2 is True calwebb_spec2 will be called, else individual steps will be ran
step_completed = False
# check if the filter is to be changed
change_filter_opaque = config.getboolean("calwebb_spec2_input_file",
"change_filter_opaque")
if change_filter_opaque:
is_filter_opaque, step_input_filename = change_filter_opaque2science.change_filter_opaque(
step_input_file, step=step)
if is_filter_opaque:
filter_opaque_msg = "With FILTER=OPAQUE, the calwebb_spec2 will run up to the extract_2d step. Resample pytest now set to Skip."
print(filter_opaque_msg)
core_utils.add_completed_steps(txt_name, step,
outstep_file_suffix,
step_completed, end_time)
pytest.skip("Skipping " + step +
" because the input file does not exist.")
if run_calwebb_spec2:
hdul = core_utils.read_hdrfits(step_output_file,
info=False,
show_hdr=False)
return hdul, step_output_file, run_pytests
else:
if run_pipe_step:
# Create the logfile for PTT, but erase the previous one if it exists
PTTcalspec2_log = os.path.join(
working_directory,
'PTT_calspec2_' + detector + '_' + step + '.log')
if os.path.isfile(PTTcalspec2_log):
os.remove(PTTcalspec2_log)
print(
"Information outputed to screen from PTT will be logged in file: ",
PTTcalspec2_log)
for handler in logging.root.handlers[:]:
logging.root.removeHandler(handler)
logging.basicConfig(filename=PTTcalspec2_log,
level=logging.INFO)
# print pipeline version
import jwst
pipeline_version = "\n *** Using jwst pipeline version: " + jwst.__version__ + " *** \n"
print(pipeline_version)
logging.info(pipeline_version)
if change_filter_opaque:
logging.info(filter_opaque_msg)
if os.path.isfile(step_input_file):
msg = " *** Step " + step + " set to True"
print(msg)
logging.info(msg)
stp = ResampleSpecStep()
# check that previous pipeline steps were run up to this point
core_utils.check_completed_steps(step, step_input_file)
# get the right configuration files to run the step
local_pipe_cfg_path = config.get(
"calwebb_spec2_input_file", "local_pipe_cfg_path")
# start the timer to compute the step running time
start_time = time.time()
if local_pipe_cfg_path == "pipe_source_tree_code":
result = stp.call(step_input_file)
else:
result = stp.call(step_input_file,
config_file=local_pipe_cfg_path +
'/resample_spec.cfg')
result.save(step_output_file)
# end the timer to compute the step running time
end_time = repr(time.time() -
start_time) # this is in seconds
msg = "Step " + step + " took " + end_time + " seconds to finish"
print(msg)
logging.info(msg)
step_completed = True
hdul = core_utils.read_hdrfits(step_output_file,
info=False,
show_hdr=False)
# rename and move the pipeline log file
try:
calspec2_pilelog = "calspec2_pipeline_" + step + "_" + detector + ".log"
pytest_workdir = os.getcwd()
logfile = glob(pytest_workdir + "/pipeline.log")[0]
os.rename(
logfile,
os.path.join(working_directory, calspec2_pilelog))
except:
IndexError
# add the running time for this step
core_utils.add_completed_steps(txt_name, step,
outstep_file_suffix,
step_completed, end_time)
return hdul, step_output_file, run_pytests
else:
msg = " The input file does not exist. Skipping step."
print(msg)
logging.info(msg)
core_utils.add_completed_steps(txt_name, step,
outstep_file_suffix,
step_completed, end_time)
pytest.skip("Skipping " + step +
" because the input file does not exist.")
else:
msg = "Skipping running pipeline step " + step
print(msg)
logging.info(msg)
end_time = core_utils.get_stp_run_time_from_screenfile(
step, detector, working_directory)
if os.path.isfile(step_output_file):
hdul = core_utils.read_hdrfits(step_output_file,
info=False,
show_hdr=False)
step_completed = True
# add the running time for this step
core_utils.add_completed_steps(txt_name, step,
outstep_file_suffix,
step_completed, end_time)
return hdul, step_output_file, run_pytests
else:
step_completed = False
# add the running time for this step
core_utils.add_completed_steps(txt_name, step,
outstep_file_suffix,
step_completed, end_time)
pytest.skip()
else:
pytest.skip("Skipping " + step +
" because data is either IFU or BOTS.")
