APT_Transforms

apt2list.py

#!/usr/bin/env python
"""
##########################################################################################
NAME: apt2list.py

AUTHOR: Nora Luetzgendorf

EXAMPLE: ./apt2list.py 'NS 4.7.2-7 NIRSpec Model (gratings)' '1132' 'Model'

DESCRIPTION:

Transforming an observation Folder of an APT file into a csv file. 

INPUTS:

obs_name:		Name of the Observation Folder)
input_xml:		Name of the Input xml file. The original APT file. This can be extracted 
				by decompressing the .aptx file

OUTPUTS:

output_csv:		Name of the Output csv which can be opened and altered with Excel and 
				transformed back to a xml file with list2apt.py
  			
##########################################################################################
"""
from lxml import etree
from astropy.table import Table, Column
from astropy.io import ascii
import argparse

##########################################################################################
# Main
##########################################################################################
#
# INPUT
parser = argparse.ArgumentParser()
parser.add_argument('obs_name',  type=str, help='Name of the Observation Folder')
parser.add_argument('input_xml',  type=str, help='Name of the Input xml file')
parser.add_argument('output_csv',  type=str, help='Name of the Input csv file')
args = parser.parse_args()
obs_name = args.obs_name
input_xml = args.input_xml
output_csv = args.output_csv

# CONSTANTS
path = "//apt:Observation[apt:Label[contains(string(), '{}')]]/apt:Template/nsil:NirspecInternalLamp/nsil:ExposureList".format(obs_name)
Mylist = {'OperatingMode': [], 'Subarray': [], 'MsaConfigFile': [], 'ReadoutPattern': [], 'Groups': [], 'Integrations': [], 'Lamp': [], 'Grating': []}

# READ
# XML file
with open('%s.xml' % input_xml) as f:
    tree = etree.parse(f)

# APT makes extensive use of XML namespaces
# (e.g. 'xmlns:nsmsasd="http://www.stsci.edu/JWST/APT/Template/NirspecMSAShortDetect"')
# so we have to as well
namespaces = tree.getroot().nsmap.copy()
# There is no 'default' namespace for XPath (used below), but the lxml parser
# does respect a default namespace, so we have to update its name from
# 'None' to 'apt'
namespaces['apt'] = namespaces[None]
del namespaces[None]

# Find your specific Observation
results = tree.xpath(path, namespaces=namespaces)
ExposureList = results[0]

# Find the Entries of the Observation
for item in Mylist:
	entryList = ExposureList.xpath('nsil:Exposure/nsil:%s' % item,namespaces=namespaces)
	for entry in entryList:
		Mylist[item].append(entry.text)


# WRITE csv file
ascii.write(Table(Mylist), '%s.csv' % output_csv, format='csv')

list2apt.py

#!/usr/bin/env python
"""
##########################################################################################
NAME: list2apt.py

AUTHOR: Nora Luetzgendorf

EXAMPLE: ./list2apt.py 'NS 4.7.2-7 NIRSpec Model (gratings)' 'Model_new' '1132' '1132_v2'

DESCRIPTION:

Transforms a csv list into an xml file that can be loaded into APT. It needs an already
existing APT file with at least one Observation to load it in. 

INPUTS:

obs_name:		Name of the Observation Folder
input_cvs:		Name of the Input csv file (the table)
input_xml:		Name of the Input xml file. The original APT file. This can be extracted 
				by decompressing the .aptx file

OUTPUTS:

output_xml:		Name of the Output xml file. This can be loaded into APT and saved as an
				.aptx file. 
  			
##########################################################################################
"""
from lxml import etree
from astropy.table import Table, Column
from astropy.io import ascii
import argparse

##########################################################################################
# Main
##########################################################################################
#
# INPUT
parser = argparse.ArgumentParser()
parser.add_argument('obs_name',  type=str, help='Name of the Observation Folder')
parser.add_argument('input_csv',  type=str, help='Name of the Input csv file')
parser.add_argument('input_xml',  type=str, help='Name of the Input xml file')
parser.add_argument('output_xml',  type=str, help='Name of the Output xml file')
args = parser.parse_args()
obs_name = args.obs_name
input_csv = args.input_csv
input_xml = args.input_xml
output_xml = args.output_xml

# CONSTANTS
path = "//apt:Observation[apt:Label[contains(string(), '{}')]]/apt:Template/nsil:NirspecInternalLamp/nsil:ExposureList".format(obs_name)
Mylist = ['OperatingMode', 'Subarray', 'MsaConfigFile', 'ReadoutPattern', 'Groups', 'Integrations', 'Lamp','Grating']

# READ
# XML file
with open('./%s.xml' % input_xml) as f:
    tree = etree.parse(f)
# CSV file 
t = ascii.read('%s.csv'% input_csv, format='csv')

# APT makes extensive use of XML namespaces
# (e.g. 'xmlns:nsmsasd="http://www.stsci.edu/JWST/APT/Template/NirspecMSAShortDetect"')
# so we have to as well
namespaces = tree.getroot().nsmap.copy()
# There is no 'default' namespace folr XPath (used below), but the lxml parser
# does respect a default namespace, so we have to update its name from
# 'None' to 'apt'
namespaces['apt'] = namespaces[None]
del namespaces[None]

# Find your specific Observation
results = tree.xpath(path, namespaces=namespaces)
ExposureList = results[0]
nExp = len(ExposureList.getchildren())

# Fill in the new values and add entries if needed
for i in range(len(t)):
	if i >= nExp:
		new_element = etree.fromstring(etree.tostring(ExposureList.xpath('//nsil:Exposure',namespaces=namespaces)[0]))
		ExposureList.append(new_element)
	for item in Mylist:
		entry = ExposureList.xpath('nsil:Exposure/nsil:%s' % item,namespaces=namespaces)[i]
		entry.text = str(t[item][i])

# WRITE Output file
tree.write('%s.xml' % output_xml)