def test_srctype2(_bigdata):
"""
Regression test of srctype step performed on MIRI LRS slitless data.
"""
suffix = 'srctyp'
output_file_base, output_file = add_suffix('srctype2_output.fits', suffix)
SourceTypeStep.call(
_bigdata +
'/miri/test_srctype/jw80600012001_02101_00003_mirimage_flat_field.fits',
output_file=output_file_base,
suffix=suffix)
h = fits.open(output_file)
href = fits.open(
_bigdata +
'/miri/test_srctype/jw80600012001_02101_00003_mirimage_srctype.fits')
newh = fits.HDUList([h['primary'], h['sci'], h['err'], h['dq']])
newhref = fits.HDUList(
[href['primary'], href['sci'], href['err'], href['dq']])
result = fits.diff.FITSDiff(newh,
newhref,
ignore_keywords=[
'DATE', 'CAL_VER', 'CAL_VCS', 'CRDS_VER',
'CRDS_CTX', 'FILENAME'
],
rtol=0.00001)
assert result.identical, result.report()
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 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.")
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
stp = SourceTypeStep()
skip_runing_pipe_step = config.getboolean("tests_only", "_".join(
(step, "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'
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 +
'/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
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.")