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IrafRed.py
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IrafRed.py
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#!/usr/bin/env python
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx #
# xxxxxxxxxxxxxxxxxxxxx-------------------PHOT0METRIC DATA REDUCTION PIPELINE-----------------xxxxxxxxxxxxxxxxxxxxxxx #
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx #
# ------------------------------------------------------------------------------------------------------------------- #
# Import Required Libraries
# ------------------------------------------------------------------------------------------------------------------- #
import os
import re
import glob
import shutil
import easygui
import numpy as np
import matplotlib.pyplot as plt
# ------------------------------------------------------------------------------------------------------------------- #
# ------------------------------------------------------------------------------------------------------------------- #
# Location Of Directories
# ------------------------------------------------------------------------------------------------------------------- #
DEFAULT_DIR = "/home/avinash/Supernovae_Data/2016gfy/"
# DIR_SNE = easygui.enterbox(msg='Enter the Location Of The Directory:', title='Directory For Reduction',
# default=DEFAULT_DIR)
DIR_SNE = "/home/avinash/Supernovae_Data/2016gfy/"
DIR_PHOT = "/home/avinash/Supernovae_Data/2016gfy/Photometry/"
DIR_SPEC = "/home/avinash/Supernovae_Data/2016gfy/Spectroscopy/"
# ------------------------------------------------------------------------------------------------------------------- #
# ------------------------------------------------------------------------------------------------------------------- #
# Useful Functions In File Handling
# ------------------------------------------------------------------------------------------------------------------- #
def remove_file(file_name):
"""
Removes the file 'file_name' in the constituent directory.
Args:
file_name : Name of the file to be removed
Returns:
None
"""
try:
os.remove(file_name)
except OSError:
pass
def remove_similar_files(common_text):
"""
Removes similar files based on the string 'common_text'.
Args:
common_text : String containing partial filename
Returns:
None
"""
for residual_files in glob.glob(common_text):
os.remove(residual_files)
def group_similar_files(text_list, common_text, exceptions=''):
"""
Groups similar files based on the string 'common_text'. Writes the similar files
onto the list 'text_list' (only if this string is not empty) and appends the similar
files to a list 'python_list'.
Args:
text_list : Name of the output text file with names grouped based on the 'common_text'
common_text : String containing partial name of the files to be grouped
exceptions : String containing the partial name of the files that need to be excluded
Returns:
list_files : Python list containing the names of the grouped files
"""
list_files = glob.glob(common_text)
if exceptions != '':
list_exception = exceptions.split(',')
for file_name in glob.glob(common_text):
for text in list_exception:
test = re.search(text, file_name)
if test:
try:
list_files.remove(file_name)
except ValueError:
pass
list_files.sort()
if len(text_list) != 0:
with open(text_list, 'w') as f:
for file_name in list_files:
f.write(file_name + '\n')
return list_files
def list_statistics(list_values):
"""
Returns the statistics of the list of elements in the input 'list_values'.
Args:
list_values : Input list of elements
Returns:
value_mean : Mean of the list of elements
value_median: Median of the list of elements
value_std : Standard Deviation of the list of elements
"""
value_mean = np.mean(list_values)
value_median = np.median(list_values)
value_std = np.std(list_values)
return value_mean, value_median, value_std
def reject(list_values, iterations=2):
"""
Rejects outliers from the input 'list_values'.
Args:
list_values : Input list of elements
iterations : No. of iterations of rejection to be run on the input list
Returns:
list_reject : Output list after rejecting outliers from the input 'list_values'
"""
list_reject = filter(lambda x: x != 'INDEF', list_values)
list_reject = [round(float(val), int(precision)) for val in list_reject]
list_reject.sort()
for _ in range(0, iterations):
if len(list_values) > 2:
value_mean, value_median, value_std = list_statistics(list_reject)
if abs(list_reject[0] - value_median) < abs(list_reject[-1] - value_median):
remove_index = -1
else:
remove_index = 0
if abs(list_reject[remove_index] - value_median) > value_std:
list_reject.pop(remove_index)
return list_reject
def text_list_to_python_list(text_list):
"""
Returns data in the file 'text_list' as a python_list.
Args:
text_list : Input file containing filenames
Returns:
python_list : List of all the elements in the file 'text_list'
Raises:
Error : File Not Found
"""
if os.path.isfile(text_list):
with open(text_list, 'r+') as f:
python_list = f.read().split()
return python_list
else:
print ("Error : File '" + text_list + "' Not Found")
def python_list_to_text_list(python_list, text_list):
"""
Put the data from the input 'python_list' to a file 'text_list' line-wise.
Args:
python_list : Name of the python_list from which data has to be read
text_list : Name of the text file onto which data has to be appended
Returns:
None
"""
with open(text_list, 'w') as f:
for element in python_list:
f.write(element + '\n')
def list_lists_to_list(list_lists, text_list):
"""
Groups filenames from a list 'list_lists' onto a single file 'text_list'.
Args:
list_lists : List containing the names of different lists
text_list : Name of the file onto which all the filenames from the 'list_lists' have to be appended
Returns:
list_files : Python list containing the names of all the constituent files
"""
list_name = []
for file_name in list_lists:
with open(file_name, 'r') as f:
file_list = f.read().split()
for element in file_list:
list_name.append(element)
python_list_to_text_list(list_files, text_list)
return list_files
def append_date(file_name, date):
"""
Appends date of observation mentioned in string 'date' to the file 'file_name' and creates a copy
of the same file.
Args:
file_name : File for which the date appended copy has to be created
date : Date of the observation of the file
Returns:
output_filename : Final name of the
"""
output_filename = date + '_' + file_name
remove_file(output_filename)
shutil.copy(file_name, output_filename)
return output_filename
def execute_script(exec_dir, python_script):
"""
Executes the python script in the mentioned directory 'home_dir'. Removes the script
from the 'home_dir' after execution.
Args:
exec_dir : Directory where the python script is to be run
python_script : Name of the python script that is to be executed
Returns:
None
"""
os.system('cp ' + python_script + ' ' + exec_dir + ' 1')
os.system('python ' + exec_dir + python_script + ' 1')
os.system('rm ' + exec_dir + python_script + ' 1')
# ------------------------------------------------------------------------------------------------------------------- #
# ------------------------------------------------------------------------------------------------------------------- #
# Collect All Folders In The Supernova Directory
# ------------------------------------------------------------------------------------------------------------------- #
list_folders = glob.glob(DIR_SNE + '*/')
list_folders.sort()
# ------------------------------------------------------------------------------------------------------------------- #
# # ------------------------------------------------------------------------------------------------------------------- #
# # Pre-Processing Of Observational Data
# # ------------------------------------------------------------------------------------------------------------------- #
# for index in range(0, len(list_folders)):
# exec_dir = DIR_SNE + list_folders[index]
# os.chdir(exec_dir)
# execute_script(exec_dir, 'pre_processing.py')
# # ------------------------------------------------------------------------------------------------------------------- #
# ------------------------------------------------------------------------------------------------------------------- #
# Prefix Photometric Object Files In A Folder With Date & Copy Photometric Files Into A New Directory 'Photometry'
# ------------------------------------------------------------------------------------------------------------------- #
# os.mkdir(str(DIR_PHOT))
for folder in list_folders:
os.chdir(folder)
date = folder[:-1].split("/")[-1]
list_object = group_similar_files('', 'fbs_2016gfy*.fits')
for file_name in list_object:
shutil.copy(file_name, date + '_' + file_name)
shutil.copy(date + '_' + file_name, DIR_PHOT)
os.chdir(DIR_SNE)
# ------------------------------------------------------------------------------------------------------------------- #
# ------------------------------------------------------------------------------------------------------------------- #
# Collecting Final Spectras
# ------------------------------------------------------------------------------------------------------------------- #
#os.chdir(DIR_SPEC)
#list_raw_folders = glob.glob('*/')
#list_folders = [date[:-1] for date in list_raw_folders if len(date[:-1]) == 5]
#list_folders.sort()
#try:
# os.mkdir(DEFAULT_DIR + 'Final_Spectra/')
#except OSError:
# pass
#for date in list_folders:
# exec_dir = DIR_SPEC + date
# os.chdir(exec_dir)
# list_cfwcbs = group_similar_files('', 'cfwcbs*.fits')
# for file_name in list_cfwcbs:
# output_filename = append_date(file_name, date)
# shutil.copy(str(output_filename), DEFAULT_DIR + 'Final_Spectra/')
# ------------------------------------------------------------------------------------------------------------------- #
# # ------------------------------------------------------------------------------------------------------------------- #
# # Alignment Of Images
# # ------------------------------------------------------------------------------------------------------------------- #
# execute_script(DIR_PHOT, 'align_dft.py')
# # ------------------------------------------------------------------------------------------------------------------- #
#
#
# # ------------------------------------------------------------------------------------------------------------------- #
# # Photometry Of Object Frames
# # ------------------------------------------------------------------------------------------------------------------- #
# execute_script(DIR_PHOT, 'photometry.py')
# # ------------------------------------------------------------------------------------------------------------------- #
#
#
# # ------------------------------------------------------------------------------------------------------------------- #
# # Spectroscopy Of Object Frames
# # ------------------------------------------------------------------------------------------------------------------- #
# execute_script(DIR_SPEC, 'spectroscopy.py')
# # ------------------------------------------------------------------------------------------------------------------- #
#
#
# # ------------------------------------------------------------------------------------------------------------------- #
# # Flux Calibration Of Final Spectras
# # ------------------------------------------------------------------------------------------------------------------- #
# execute_script(DIR_SPEC, 'fluxcalib.py')
# # ------------------------------------------------------------------------------------------------------------------- #