def output_hdul(set_inandout_filenames, config):
# determine if the pipeline is to be run in full, per steps, or skipped
run_calwebb_spec2 = config.get("run_calwebb_spec2_in_full", "run_calwebb_spec2")
if run_calwebb_spec2 == "skip":
print('\n * PTT finished processing run_calwebb_spec2 is set to skip. \n')
pytest.exit("Skipping pipeline run and tests for spec2, run_calwebb_spec2 is set to skip in PTT_config file.")
elif "T" in run_calwebb_spec2:
run_calwebb_spec2 = True
else:
run_calwebb_spec2 = False
# get the general info
set_inandout_filenames_info = core_utils.read_info4outputhdul(config, set_inandout_filenames)
step, txt_name, step_input_file, step_output_file, outstep_file_suffix = set_inandout_filenames_info
# determine which steps are to be run, if not run in full
run_pipe_step = config.getboolean("run_pipe_steps", step)
# determine which tests are to be run
bkg_subtract_completion_tests = config.getboolean("run_pytest", "_".join((step, "completion", "tests")))
bkg_subtract_numerical_tests = config.getboolean("run_pytest", "_".join((step, "numerical", "tests")))
#bkg_subtract_validation_tests = config.getboolean("run_pytest", "_".join((step, "validation", "tests")))
run_pytests = [bkg_subtract_completion_tests, bkg_subtract_numerical_tests]#, bkg_subtract_validation_tests]
# if run_calwebb_spec2 is True calwebb_spec2 will be called, else individual steps will be ran
step_completed = False
end_time = '0.0'
# skip if BOTS data, else perform step
output_directory = config.get("calwebb_spec2_input_file", "output_directory")
initial_input_file = config.get("calwebb_spec2_input_file", "input_file")
initial_input_file = os.path.join(output_directory, initial_input_file)
detector = fits.getval(initial_input_file, "DETECTOR", 0)
calspec2_pilelog = "calspec2_pipeline_" + step + "_" + detector + ".log"
pytest_workdir = TESTSDIR
if os.path.isfile(initial_input_file):
inhdu = core_utils.read_hdrfits(initial_input_file, info=False, show_hdr=False)
else:
pytest.skip("Skipping "+step+" because the initial input file given in PTT_config.cfg does not exist.")
if not core_utils.check_BOTS_true(inhdu):
if run_calwebb_spec2:
if os.path.isfile(step_output_file):
hdul = core_utils.read_hdrfits(step_output_file, info=False, show_hdr=False)
else:
pytest.skip("Skipping "+step+" because the output file does not exist.")
return hdul, step_output_file, step_input_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(output_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 os.path.isfile(step_input_file):
msg = " The input file "+step_input_file+" exists... will run step "+step
print(msg)
logging.info(msg)
bkg_list = core_utils.getlist("additional_arguments", "bkg_list")
existing_bgfiles = 0
for bg_file in bkg_list:
if os.path.isfile(bg_file):
existing_bgfiles += 1
if existing_bgfiles == 0:
msg = " Need at least one background file to continue. Step will be skipped."
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 files listed on bkg_list in the configuration "
"file do not exist.")
else:
# continue since the file(s) exist
msg = "*** Step "+step+" set to True"
print(msg)
logging.info(msg)
stp = BackgroundStep()
# 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()
print("running pipeline...")
if local_pipe_cfg_path == "pipe_source_tree_code":
result = stp.call(step_input_file, bkg_list)
else:
result = stp.call(step_input_file, bkg_list, config_file=local_pipe_cfg_path+'/background.cfg')
if result is not None:
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)
hdul = core_utils.read_hdrfits(step_output_file, info=False, show_hdr=False)
step_completed = True
# rename and move the pipeline log file
pipelog = "pipeline_" + detector + ".log"
try:
calspec2_pilelog = "calspec2_pipeline_" + step + "_" + detector + ".log"
pytest_workdir = TESTSDIR
logfile = glob(pytest_workdir + "/" + pipelog)[0]
os.rename(logfile, os.path.join(output_directory, calspec2_pilelog))
except IndexError:
print("\n* WARNING: Something went wrong. Could not find a ", pipelog, " file \n")
# 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, step_input_file, run_pytests
else:
print(" The input file does not exist. Skipping step.")
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, output_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, step_input_file, run_pytests
else:
# add the running time for this step
core_utils.add_completed_steps(txt_name, step, outstep_file_suffix, step_completed, end_time)
pytest.skip("Test skipped because input file "+step_output_file+" does not exist.")
else:
msg = "Skipping "+step+" because data is BOTS."
print(msg)
logging.info(msg)
core_utils.add_completed_steps(txt_name, step, outstep_file_suffix, step_completed, end_time)
pytest.skip(msg)
def validate_flat_field(output_hdul):
hdu = output_hdul[0]
step_output_file, msa_shutter_conf, dflat_path, sflat_path, fflat_path = output_hdul[
2]
flattest_threshold_diff, save_flattest_plot, write_flattest_files = output_hdul[
3]
# show the figures
show_figs = False
log_msgs = None
# determine the testing mode
do_fs_flattest = False
if core_utils.check_FS_true(hdu) or core_utils.check_BOTS_true(hdu):
do_fs_flattest = True
elif 'bots' in step_output_file.lower() or 'fs' in step_output_file.lower(
):
do_fs_flattest = True
do_mos_flattest = False
if core_utils.check_MOS_true(hdu) or 'mos' in step_output_file.lower():
do_mos_flattest = True
do_ifu_flattest = False
if core_utils.check_IFU_true(hdu) or 'ifu' in step_output_file.lower():
do_ifu_flattest = True
# run the test
if do_fs_flattest:
median_diff, result_msg, log_msgs = flattest_fs.flattest(
step_output_file,
dflat_path=dflat_path,
sflat_path=sflat_path,
fflat_path=fflat_path,
writefile=write_flattest_files,
show_figs=show_figs,
save_figs=save_flattest_plot,
interpolated_flat=None,
threshold_diff=flattest_threshold_diff,
output_directory=None,
debug=False)
elif do_mos_flattest:
median_diff, result_msg, log_msgs = flattest_mos.flattest(
step_output_file,
dflat_path=dflat_path,
sflat_path=sflat_path,
fflat_path=fflat_path,
msa_shutter_conf=msa_shutter_conf,
writefile=write_flattest_files,
show_figs=show_figs,
save_figs=save_flattest_plot,
interpolated_flat=None,
threshold_diff=flattest_threshold_diff,
debug=False)
elif do_ifu_flattest:
median_diff, result_msg, log_msgs = flattest_ifu.flattest(
step_output_file,
dflat_path=dflat_path,
sflat_path=sflat_path,
fflat_path=fflat_path,
writefile=write_flattest_files,
mk_all_slices_plt=False,
show_figs=show_figs,
save_figs=save_flattest_plot,
interpolated_flat=None,
threshold_diff=flattest_threshold_diff,
debug=False)
else:
pytest.skip(
"Skipping pytest: The input fits file is not FS, MOS, or IFU. This tool does not yet include the "
"routine to verify this kind of file.")
if log_msgs is not None:
for msg in log_msgs:
logging.info(msg)
if median_diff == "skip":
logging.info(result_msg)
pytest.skip(result_msg)
else:
print(result_msg)
logging.info(result_msg)
return median_diff
def validate_pathloss(output_hdul):
hdu = output_hdul[0]
step_input_filename = output_hdul[2]
comparison_filename = output_hdul[1]
threshold_diff, save_figs, writefile = output_hdul[4]
# other default variables
show_figs = False
log_msgs = None
debug = False
# determine the type of source
srouce_type = fits.getval(comparison_filename, "SRCTYPE", "SCI", 1)
msg = "Source type is: " + srouce_type
print(msg)
logging.info(msg)
# get the corresponding reference file
reffile = hdu["R_PTHLOS"].replace("crds://", "")
# download the file if necessary
if not os.path.isfile(reffile):
reffile_url = "https://jwst-crds.stsci.edu/unchecked_get/references/jwst/" + reffile
urllib.request.urlretrieve(reffile_url, reffile)
if core_utils.check_FS_true(hdu) or core_utils.check_BOTS_true(hdu):
if "point" in srouce_type.lower():
median_diff, result_msg, log_msgs = pathloss_fs_ps.pathtest(
step_input_filename,
reffile,
comparison_filename,
writefile=writefile,
show_figs=show_figs,
save_figs=save_figs,
threshold_diff=threshold_diff,
debug=debug)
elif "extend" in srouce_type.lower():
median_diff, result_msg, log_msgs = pathloss_fs_uni.pathtest(
step_input_filename,
reffile,
comparison_filename,
writefile=writefile,
show_figs=show_figs,
save_figs=save_figs,
threshold_diff=threshold_diff,
debug=debug)
elif core_utils.check_MOS_true(hdu):
if "point" in srouce_type.lower():
median_diff, result_msg, log_msgs = pathloss_mos_ps.pathtest(
step_input_filename,
reffile,
comparison_filename,
writefile=writefile,
show_figs=show_figs,
save_figs=save_figs,
threshold_diff=threshold_diff,
debug=debug)
elif "extend" in srouce_type.lower():
median_diff, result_msg, log_msgs = pathloss_mos_uni.pathtest(
step_input_filename,
reffile,
comparison_filename,
writefile=writefile,
show_figs=show_figs,
save_figs=save_figs,
threshold_diff=threshold_diff,
debug=debug)
elif core_utils.check_IFU_true(hdu):
if "point" in srouce_type.lower():
median_diff, result_msg, log_msgs = pathloss_ifu_ps.pathtest(
step_input_filename,
reffile,
comparison_filename,
writefile=writefile,
show_figs=show_figs,
save_figs=save_figs,
threshold_diff=threshold_diff,
debug=debug)
elif "extend" in srouce_type.lower():
median_diff, result_msg, log_msgs = pathloss_ifu_uni.pathtest(
step_input_filename,
reffile,
comparison_filename,
writefile=writefile,
show_figs=show_figs,
save_figs=save_figs,
threshold_diff=threshold_diff,
debug=debug)
else:
pytest.skip(
"Skipping pytest: The input fits file is not FS, MOS, or IFU. This tool does not yet include the "
"routine to verify this kind of file.")
if log_msgs is not None:
for msg in log_msgs:
logging.info(msg)
if median_diff == "skip":
logging.info(result_msg)
pytest.skip(result_msg)
else:
print(result_msg)
logging.info(result_msg)
return median_diff
def output_hdul(set_inandout_filenames, config):
# determine if the pipeline is to be run in full, per steps, or skipped
run_calwebb_spec2 = config.get("run_calwebb_spec2_in_full",
"run_calwebb_spec2")
if run_calwebb_spec2 == "skip":
print(
'\n * PTT finished processing run_calwebb_spec2 is set to skip. \n'
)
pytest.exit(
"Skipping pipeline run and tests for spec2, run_calwebb_spec2 is set to skip in PTT_config file."
)
elif "T" in run_calwebb_spec2:
run_calwebb_spec2 = True
else:
run_calwebb_spec2 = False
# get the general info
set_inandout_filenames_info = core_utils.read_info4outputhdul(
config, set_inandout_filenames)
step, txt_name, step_input_file, step_output_file, outstep_file_suffix = set_inandout_filenames_info
run_pipe_step = config.getboolean("run_pipe_steps", step)
# determine which tests are to be run
pathloss_completion_tests = config.getboolean(
"run_pytest", "_".join((step, "completion", "tests")))
pathloss_reffile_tests = config.getboolean(
"run_pytest", "_".join((step, "reffile", "tests")))
pathloss_validation_tests = config.getboolean(
"run_pytest", "_".join((step, "validation", "tests")))
run_pytests = [
pathloss_completion_tests, pathloss_reffile_tests,
pathloss_validation_tests
]
pathloss_threshold_diff = config.get("additional_arguments",
"pathloss_threshold_diff")
save_flattest_plot = config.getboolean("additional_arguments",
"save_pathloss_plot")
write_flattest_files = config.getboolean("additional_arguments",
"write_pathloss_files")
pathloss_switches = [
pathloss_threshold_diff, save_flattest_plot, write_flattest_files
]
# if run_calwebb_spec2 is True calwebb_spec2 will be called, else individual steps will be ran
step_completed = False
end_time = '0.0'
# 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. " \
"Pathloss 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 FILTER=OPAQUE.")
# only run this step if data is not BOTS
output_directory = config.get("calwebb_spec2_input_file",
"output_directory")
initial_input_file = config.get("calwebb_spec2_input_file", "input_file")
initial_input_file = os.path.join(output_directory, initial_input_file)
if os.path.isfile(initial_input_file):
inhdu = core_utils.read_hdrfits(initial_input_file,
info=False,
show_hdr=False)
detector = fits.getval(initial_input_file, "DETECTOR", 0)
else:
pytest.skip(
"Skipping " + step +
" because the initial input file given in PTT_config.cfg does not exist."
)
if not core_utils.check_BOTS_true(inhdu):
if run_calwebb_spec2:
hdul = core_utils.read_hdrfits(step_output_file,
info=False,
show_hdr=False)
return hdul, step_output_file, step_input_file, run_pytests, pathloss_switches
else:
if run_pipe_step:
# Create the logfile for PTT, but erase the previous one if it exists
PTTcalspec2_log = os.path.join(
output_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 = PathLossStep()
# 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 +
'/pathloss.cfg')
result.save(step_output_file)
# For the moment, the pipeline is using the wrong reference file for slit 400A1, so the
# file needs to be re-processed with the right reference file BUT we are
# skipping this slit
"""
if core_utils.check_FS_true(inhdu):
print("\n * WARNING: For the moment, the wrong reference file is being used for "
"processing slit 400A1. The file will be re-processed ")
# The file can manually be re-run with
# $ strun jwst.pathloss.PathLossStep final_output_caldet1_NRS1_srctype.fits
# --override_pathloss=jwst-nirspec-a400.plrf.fits
pathloss_400a1 = step_input_file.replace("srctype.fits", "pathloss_400A1.fits")
reffile_400a1 = "jwst-nirspec-a400.plrf.fits"
print("Re-processing slit with new reference file: ", reffile_400a1)
pl = PathLossStep()
pl.override_pathloss = reffile_400a1
pl_result = pl.run(step_input_file)
pl_result.save(pathloss_400a1)
#import subprocess
#subprocess.run(["mv", step_input_file.replace("srctype", "pathlossstep"), pathloss_400a1])
print("Saved pipeline re-processed file as: ", pathloss_400a1)
"""
# end the timer to compute calwebb_spec2 running time
end_time = repr(time.time() -
start_time) # this is in seconds
msg = " * calwebb_spec2 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
pipelog = "pipeline_" + detector + ".log"
try:
calspec2_pilelog = "calspec2_pipeline_" + step + "_" + detector + ".log"
pytest_workdir = TESTSDIR
logfile = glob(pytest_workdir + "/" + pipelog)[0]
os.rename(
logfile,
os.path.join(output_directory, calspec2_pilelog))
except IndexError:
print(
"\n* WARNING: Something went wrong. Could not find a ",
pipelog, " file \n")
# 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, step_input_file, run_pytests, pathloss_switches
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, output_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, step_input_file, run_pytests, pathloss_switches
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("Test skipped because input file " +
step_output_file + " does not exist.")
else:
pytest.skip("Skipping " + step + " because data is BOTS.")
def output_hdul(set_inandout_filenames, config):
# determine if the pipeline is to be run in full, per steps, or skipped
run_calwebb_spec2 = config.get("run_calwebb_spec2_in_full",
"run_calwebb_spec2")
if run_calwebb_spec2 == "skip":
print(
'\n * PTT finished processing run_calwebb_spec2 is set to skip. \n'
)
pytest.exit(
"Skipping pipeline run and tests for spec2, run_calwebb_spec2 is set to skip in PTT_config file."
)
elif "T" in run_calwebb_spec2:
run_calwebb_spec2 = True
else:
run_calwebb_spec2 = False
# get the general info
set_inandout_filenames_info = core_utils.read_info4outputhdul(
config, set_inandout_filenames)
step, txt_name, step_input_file, step_output_file, outstep_file_suffix = set_inandout_filenames_info
run_pipe_step = config.getboolean("run_pipe_steps", step)
# determine which tests are to be run
run_pytests = config.getboolean("run_pytest", "_".join(
(step, "completion", "tests")))
# if run_calwebb_spec2 is True calwebb_spec2 will be called, else individual steps will be ran
step_completed = False
end_time = '0.0'
# 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. Source " \
"Type 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 FILTER=OPAQUE.")
# only run this step if data is not BOTS
output_directory = config.get("calwebb_spec2_input_file",
"output_directory")
initial_input_file = config.get("calwebb_spec2_input_file", "input_file")
initial_input_file = os.path.join(output_directory, initial_input_file)
if os.path.isfile(initial_input_file):
inhdu = core_utils.read_hdrfits(initial_input_file,
info=False,
show_hdr=False)
detector = fits.getval(initial_input_file, "DETECTOR", 0)
else:
pytest.skip(
"Skipping " + step +
" because the initial input file given in PTT_config.cfg does not exist."
)
if not core_utils.check_BOTS_true(inhdu):
if run_calwebb_spec2:
hdul = core_utils.read_hdrfits(step_output_file,
info=False,
show_hdr=False)
scihdul = core_utils.read_hdrfits(step_output_file,
info=False,
show_hdr=False,
ext=1)
return hdul, step_output_file, run_pytests, scihdul
else:
if run_pipe_step:
# Create the logfile for PTT, but erase the previous one if it exists
PTTcalspec2_log = os.path.join(
output_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 = SourceTypeStep()
# 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 +
'/srctype.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)
scihdul = core_utils.read_hdrfits(step_output_file,
info=False,
show_hdr=False,
ext=1)
# rename and move the pipeline log file
pipelog = "pipeline_" + detector + ".log"
try:
calspec2_pilelog = "calspec2_pipeline_" + step + "_" + detector + ".log"
pytest_workdir = TESTSDIR
logfile = glob(pytest_workdir + "/" + pipelog)[0]
os.rename(
logfile,
os.path.join(output_directory, calspec2_pilelog))
except IndexError:
print(
"\n* WARNING: Something went wrong. Could not find a ",
pipelog, " file \n")
# 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, scihdul
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, output_directory)
if os.path.isfile(step_output_file):
hdul = core_utils.read_hdrfits(step_output_file,
info=False,
show_hdr=False)
scihdul = core_utils.read_hdrfits(step_output_file,
info=False,
show_hdr=False,
ext=1)
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, scihdul
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("Test skipped because input file " +
step_output_file + " does not exist.")
else:
pytest.skip("Skipping " + step + " because data is BOTS.")