#!/usr/bin/env python


# compatibility with python 2/3:
from __future__ import print_function
from __future__ import division

import sys, os
import glob
import time
import datetime
import numpy as np
import astropy.io.fits as pyfits

import argparse
import pkg_resources
import appdirs

# Directory of this file
path = os.path.dirname(os.path.realpath(__file__))

# Global variables
#import ac_settings as ac_set

# Global variables
from .actin_files import ac_settings as ac_set

from .actin_files import ac_config
from .actin_files import ac_read_data
from .actin_files import ac_get_win
from .actin_files import ac_calc_ind
from .actin_files import ac_save
from .actin_files import ac_plot_time as ac_plot
from .actin_files import ac_tools

from matplotlib import pylab as plt


# initiate global variables:
ac_set.init()
# Configuration file:
config_file = os.path.join(path, "config_lines.txt")
# Version file:
version_file = os.path.join(path, "VERSION")
# Print preamble:
version = ac_set.preamble(version_file)


def actin_file(file, calc_index=None, rv_in=None, config_file=config_file, save_output=False, ln_plts=False, obj_name=None, targ_list=None, del_out=False, frac=True):
    """
    Runs ACTIN for one fits file.
    Accepts files of types: 'S2D', 'S1D', 'e2ds', 's1d', 's1d_*_rv', 'ADP', and 'rdb'.
    Recognizes fits files from HARPS, HARPS-N and ESPRESSO instruments.
    """

    print()
    print("--------------------")
    print("EXECUTING ACTIN_FILE")
    print("--------------------")

    if type(file) is list: file = file[0]

    # Check if file is from known instrument
    tel, instr = ac_tools.get_instr(file)
    if instr == False: pass
    elif instr in ac_set.instr: pass
    else:
        msg="*** ERROR:\nUnrecognized instrument. ACTIN only accepts HARPS, HARPS-N or ESPRESSO. To read from a different instrument convert data to rdb file with the headers: 'obj', 'obs_date', 'bjd', 'wave', 'flux', 'error_pixel' (optional)."
        sys.exit(msg)

    # Checking if object in targ_list is the same as the object in fits file
    if targ_list:
        check = ac_tools.check_targ(file, targets=targ_list)
        if check is True: pass
        elif check is False: return

    # Read config file and retrieve lines information
    if calc_index:
        sel_lines = ac_config.read_conf(config_file, calc_index)

    # Read data from file
    data = ac_read_data.read_data(file, rv_in=rv_in, obj_name=obj_name)

    if not data:
        return

    # Check output file for duplicates
    if save_output is not False and data['file_type'] != "rdb":
        dupl = ac_save.check_duplicate(data['obj'], data['obs_date'], data['instr'], data['file_type'], save_output)
        if dupl is True: return

    if calc_index:
        # Check selected lines for spectral range and orders
        test = ac_calc_ind.check_lines(data['wave'], sel_lines)
        if not test:
            print("*** ACTION: Ignoring measurement.")
            return

        # Calculate flux in the required lines
        sel_lines = ac_calc_ind.calc_flux_lines(data, sel_lines, ln_plts=ln_plts, frac=frac)

        # Calculate chosen indices
        index = ac_calc_ind.calc_ind(sel_lines)
    if not calc_index:
        index = None
        sel_lines = None

    # Write output to rdb file in "out_dir"/"obj"
    if save_output is not False:
        rdb_file = ac_save.save_data(data, index, out_dir=save_output)
    else: rdb_file = None

    info = {}
    info['config_file'] = config_file
    info['file_type']   = data['file_type']
    info['version']     = version
    info['source_path'] = os.path.split(file)[0]
    info['tel']         = data['tel']
    info['instr']       = data['instr']
    info['obj']         = data['obj']

    options = {}
    options['frac'] = frac

    output = {}
    output['data']      = data
    output['index']     = index
    output['sel_lines'] = sel_lines
    output['info']      = info
    output['options']   = options
    output['rdb_file']  = rdb_file

    return output


def actin(files, calc_index=None, rv_in=None, config_file=None, save_output=False, ln_plts=False, obj_name=None, targ_list=None, del_out=False, frac=True, test=False, save_plots=False):
    """
    Runs 'actin_file' function for one or multiple fits files, for one or multiple stars.
    Accepts fits files from HARPS, HARPS-N, and ESPRESSO instruments.
    Accepts files of types: 'S1D', 'S2D', 'e2ds', 's1d', 's1d_*_rv', 'ADP', and 'rdb'.
    """

    print()
    print("----------------")
    print(" STARTING ACTIN ")
    print("----------------")

    start_time = time.time()

    # Get config file from installation or input
    if config_file is None:
        cfg_file = get_config()
    else:
        cfg_file = config_file
    print()
    print("Using spectral lines from configuration file:")
    print(cfg_file)

    # test values can be 'S1D', 'S2D', 'e2ds', 's1d', 'adp', or 'rdb'
    # this needs to have before anything that uses 'files'
    if test:
        calc_index, files = ac_tools.test_actin(test, path, calc_index)

    if not files:
        raise Exception("*** ERROR: There are no files to read")

    # Make lists to be iterated below
    if isinstance(files, str): files = [files]

    if rv_in is None:
        rv_in = [rv_in]*len(files)
    elif type(rv_in) is not list:
        rv_in = [float(rv_in)] ### added float to use as module
    else: pass

    # Check if files exist
    ac_tools.check_files(files)

    # Remove output file
    if del_out:
        print()
        print("Executing ac_tools.remove_output:")
        print("Searching output files to delete...")
        #ac_tools.remove_output(files, save_output, targ_list)
        if obj_name:
            for f in files:
                _, instr = ac_tools.get_instr(f)
                file_type = ac_tools.get_file_type(f)
                if isinstance(obj_name, str):
                    star_name = obj_name
                    ac_tools.remove_output2(star_name, instr, file_type, save_output)
                elif isinstance(obj_name, (list, np.ndarray)):
                    for star_name in obj_name:
                        ac_tools.remove_output2(star_name, instr, file_type, save_output)
        elif not obj_name:
            for f in files:
                star_name = ac_tools.get_target(f)
                _, instr = ac_tools.get_instr(f)
                file_type = ac_tools.get_file_type(f)
                ac_tools.remove_output2(star_name, instr, file_type, save_output)

    # Option to make line plots directory the same as the data output dir
    if ln_plts == 'same':
        ln_plts = save_output

    total_files = len(files)

    # Organize files by path to star and file type
    files_list = ac_tools.files_by_star_and_ftype(files)

    n_files_t = 0
    # star directories
    for k in range(len(files_list)):
        # file types
        for i in range(len(files_list[k])):
            n_files = 0
            # files organized by dir and file type
            for j in range(len(files_list[k][i])):
                n_files += 1
                n_files_t += 1
                # Run actin file
                output = actin_file(files_list[k][i][j],
                                    calc_index,
                                    rv_in=rv_in[j],
                                    config_file=cfg_file,
                                    save_output=save_output,
                                    ln_plts=ln_plts,
                                    obj_name=obj_name,
                                    targ_list=targ_list,
                                    del_out=del_out,
                                    frac=frac)

            # POST-PROCESSING:
            if output:
                # Dictionaries for each file type
                sel_lines = output['sel_lines']
                info = output['info']
                options = output['options']
                rdb_file = output['rdb_file']

                # Save log and line info files
                ac_save.save_log(info, options, n_files, out_dir=save_output)
                ac_save.save_line_info(info, sel_lines, out_dir=save_output)

                if save_plots:
                    # Save time-series plots
                    ac_plot.plt_time(info, out_dir=save_output, rmv_flgs=False, save_plt=True)
                    ac_plot.plt_time_mlty(info, out_dir=save_output, rmv_flgs=False, save_plt=True, hdrs=calc_index)
            else: pass

    if n_files_t != total_files:
        print()
        print("*** ERROR: Number of ACTIN calls different than number of files.")
        print("n_files_t:", n_files_t)
        print("total_files:", total_files)

    elapsed_time = (time.time() - start_time)/60

    # Summary:
    print("\n---------------------------------")
    print("Fractional pixels:\t{}".format(frac))
    print("Files analysed:\t\t{}".format(total_files))
    print("Save output:\t\t{}".format(save_output))
    print("Elapsed time:\t\t{:.4f} min".format(elapsed_time))

    return


def get_config():
    """
    Check for existence of ACTIN folder and config file and creates them if not present. Returns the path to the config file.
    """
    cfg_dir = appdirs.user_config_dir('ACTIN')
    if not os.path.exists(cfg_dir):
        os.makedirs(cfg_dir)
    cfg_file = os.path.join(cfg_dir, 'config_lines.txt')
    if not os.path.isfile(cfg_file):
        create_user_config(cfg_file)

    return cfg_file


def create_user_config(cfg_file):
    """
    Create the user's config file
    """
    from shutil import copyfile ###
    src = pkg_resources.resource_stream(__name__, 'config_lines.txt')
    copyfile(src.name, cfg_file)



def main():
    """
    Main function, call actin function with arguments from terminal.
    """

    # initiate the parser
    parser = argparse.ArgumentParser()

    # add short and long argument
    parser.add_argument('--files', '-f', help='Read file(s)', nargs='+')

    parser.add_argument('--calc_index', '-i', help="Index id to calculate as designated by 'ind_id' in config_index.txt.", nargs='+', default=None)

    parser.add_argument('--rv_in', '-rv', help="RV value to calibrate wavelength. If False (default) try to read RV from CCF file.", nargs='+', default=None, type=float)

    parser.add_argument('--config_file', '-cf', help='Path to config_file, or False (default) read config file from standard directory.', default=None)

    parser.add_argument('--save_output', '-s', help='Path to output directory of data table, or False (default).', default=False)

    parser.add_argument('--ln_plts', '-lp', help="Path to directory to save line plots. If 'same' saves line plots to same directory of data output. If 'show' only shows the plots. If 'False' (default) does not save or show line plots", default=False)

    parser.add_argument('--obj_name', '-obj', help='Give target a name that overides the one from the fits files.', default=None)

    parser.add_argument('--targ_list', '-tl', help='Give a list of stars to select from fits files.', nargs='+', default=None)

    parser.add_argument('--del_out', '-del', help='Delete output data file if True.', default=False, type=lambda x: (str(x).lower() == 'true'))

    parser.add_argument('--test', '-t', help='Tests actin using the provided fits files in the "test_files" directory. Options are "e2ds", "s1d", and "adp"', default=False)

    parser.add_argument('--frac', '-frc', help='Turns fractional pixel on (True, default) or off (False).', default=True, type=lambda x: (str(x).lower() == 'true'))

    parser.add_argument('--save_plots', '-sp', help="If True saves time-series and multi-plots to same directory as 'save_output'.", default=False, type=lambda x: (str(x).lower() == 'true'))


    # read arguments from the command lines
    args = parser.parse_args()

    actin(files       = args.files,
          calc_index  = args.calc_index,
          rv_in       = args.rv_in,
          config_file = args.config_file,
          save_output = args.save_output,
          ln_plts     = args.ln_plts,
          obj_name    = args.obj_name,
          targ_list   = args.targ_list,
          del_out     = args.del_out,
          test        = args.test,
          frac        = args.frac,
          save_plots  = args.save_plots)

if __name__ == "__main__":
    ac_set.preamble(version_file, verbose=True)
    main()

#!/usr/bin/env python


# compatibility with python 2/3:
from __future__ import print_function
from __future__ import division

import sys, os
import glob
import time
import datetime
import numpy as np
import astropy.io.fits as pyfits

import argparse
import pkg_resources
import appdirs

# Directory of this file
path = os.path.dirname(os.path.realpath(__file__))

# Global variables
#import ac_settings as ac_set

# Global variables
from .actin_files import ac_settings as ac_set

from .actin_files import ac_config
from .actin_files import ac_read_data
from .actin_files import ac_get_win
from .actin_files import ac_calc_ind
from .actin_files import ac_save
from .actin_files import ac_plot_time as ac_plot
from .actin_files import ac_tools

from matplotlib import pylab as plt


# initiate global variables:
ac_set.init()
# Configuration file:
config_file = os.path.join(path, "config_lines.txt")
# Version file:
version_file = os.path.join(path, "VERSION")
# Print preamble:
version = ac_set.preamble(version_file)


def actin_file(file, calc_index=None, rv_in=None, config_file=config_file, save_output=False, ln_plts=False, obj_name=None, targ_list=None, del_out=False, frac=True):
    """
    Runs ACTIN for one fits file.
    Accepts files of types: 'S2D', 'S1D', 'e2ds', 's1d', 's1d_*_rv', 'ADP', and 'rdb'.
    Recognizes fits files from HARPS, HARPS-N and ESPRESSO instruments.
    """

    print()
    print("--------------------")
    print("EXECUTING ACTIN_FILE")
    print("--------------------")

    if type(file) is list: file = file[0]

    # Check if file is from known instrument
    tel, instr = ac_tools.get_instr(file)
    if instr == False: pass
    elif instr in ac_set.instr: pass
    else:
        msg="*** ERROR:\nUnrecognized instrument. ACTIN only accepts HARPS, HARPS-N or ESPRESSO. To read from a different instrument convert data to rdb file with the headers: 'obj', 'obs_date', 'bjd', 'wave', 'flux', 'error_pixel' (optional)."
        sys.exit(msg)

    # Checking if object in targ_list is the same as the object in fits file
    if targ_list:
        check = ac_tools.check_targ(file, targets=targ_list)
        if check is True: pass
        elif check is False: return

    # Read config file and retrieve lines information
    if calc_index:
        sel_lines = ac_config.read_conf(config_file, calc_index)

    # Read data from file
    data = ac_read_data.read_data(file, rv_in=rv_in, obj_name=obj_name)

    if not data:
        return

    # Check output file for duplicates
    if save_output is not False and data['file_type'] != "rdb":
        dupl = ac_save.check_duplicate(data['obj'], data['obs_date'], data['instr'], data['file_type'], save_output)
        if dupl is True: return

    if calc_index:
        # Check selected lines for spectral range and orders
        test = ac_calc_ind.check_lines(data['wave'], sel_lines)
        if not test:
            print("*** ACTION: Ignoring measurement.")
            return

        # Calculate flux in the required lines
        sel_lines = ac_calc_ind.calc_flux_lines(data, sel_lines, ln_plts=ln_plts, frac=frac)

        # Calculate chosen indices
        index = ac_calc_ind.calc_ind(sel_lines)
    if not calc_index:
        index = None
        sel_lines = None

    # Write output to rdb file in "out_dir"/"obj"
    if save_output is not False:
        rdb_file = ac_save.save_data(data, index, out_dir=save_output)
    else: rdb_file = None

    info = {}
    info['config_file'] = config_file
    info['file_type']   = data['file_type']
    info['version']     = version
    info['source_path'] = os.path.split(file)[0]
    info['tel']         = data['tel']
    info['instr']       = data['instr']
    info['obj']         = data['obj']

    options = {}
    options['frac'] = frac

    output = {}
    output['data']      = data
    output['index']     = index
    output['sel_lines'] = sel_lines
    output['info']      = info
    output['options']   = options
    output['rdb_file']  = rdb_file

    return output


def actin(files, calc_index=None, rv_in=None, config_file=None, save_output=False, ln_plts=False, obj_name=None, targ_list=None, del_out=False, frac=True, test=False, save_plots=False):
    """
    Runs 'actin_file' function for one or multiple fits files, for one or multiple stars.
    Accepts fits files from HARPS, HARPS-N, and ESPRESSO instruments.
    Accepts files of types: 'S1D', 'S2D', 'e2ds', 's1d', 's1d_*_rv', 'ADP', and 'rdb'.
    """

    print()
    print("----------------")
    print(" STARTING ACTIN ")
    print("----------------")

    start_time = time.time()

    # Get config file from installation or input
    if config_file is None:
        cfg_file = get_config()
    else:
        cfg_file = config_file
    print()
    print("Using spectral lines from configuration file:")
    print(cfg_file)

    # test values can be 'S1D', 'S2D', 'e2ds', 's1d', 'adp', or 'rdb'
    # this needs to have before anything that uses 'files'
    if test:
        calc_index, files = ac_tools.test_actin(test, path, calc_index)

    if not files:
        raise Exception("*** ERROR: There are no files to read")

    # Make lists to be iterated below
    if isinstance(files, str): files = [files]

    if rv_in is None:
        rv_in = [rv_in]*len(files)
    elif type(rv_in) is not list:
        rv_in = [float(rv_in)] ### added float to use as module
    else: pass

    # Check if files exist
    ac_tools.check_files(files)

    # Remove output file
    if del_out:
        print()
        print("Executing ac_tools.remove_output:")
        print("Searching output files to delete...")
        #ac_tools.remove_output(files, save_output, targ_list)
        if obj_name:
            for f in files:
                _, instr = ac_tools.get_instr(f)
                file_type = ac_tools.get_file_type(f)
                if isinstance(obj_name, str):
                    star_name = obj_name
                    ac_tools.remove_output2(star_name, instr, file_type, save_output)
                elif isinstance(obj_name, (list, np.ndarray)):
                    for star_name in obj_name:
                        ac_tools.remove_output2(star_name, instr, file_type, save_output)
        elif not obj_name:
            for f in files:
                star_name = ac_tools.get_target(f)
                _, instr = ac_tools.get_instr(f)
                file_type = ac_tools.get_file_type(f)
                ac_tools.remove_output2(star_name, instr, file_type, save_output)

    # Option to make line plots directory the same as the data output dir
    if ln_plts == 'same':
        ln_plts = save_output

    total_files = len(files)

    # Organize files by path to star and file type
    files_list = ac_tools.files_by_star_and_ftype(files)

    n_files_t = 0
    # star directories
    for k in range(len(files_list)):
        # file types
        for i in range(len(files_list[k])):
            n_files = 0
            # files organized by dir and file type
            for j in range(len(files_list[k][i])):
                n_files += 1
                n_files_t += 1
                # Run actin file
                output = actin_file(files_list[k][i][j],
                                    calc_index,
                                    rv_in=rv_in[j],
                                    config_file=cfg_file,
                                    save_output=save_output,
                                    ln_plts=ln_plts,
                                    obj_name=obj_name,
                                    targ_list=targ_list,
                                    del_out=del_out,
                                    frac=frac)

            # POST-PROCESSING:
            if output:
                # Dictionaries for each file type
                sel_lines = output['sel_lines']
                info = output['info']
                options = output['options']
                rdb_file = output['rdb_file']

                # Save log and line info files
                ac_save.save_log(info, options, n_files, out_dir=save_output)
                ac_save.save_line_info(info, sel_lines, out_dir=save_output)

                if save_plots:
                    # Save time-series plots
                    ac_plot.plt_time(info, out_dir=save_output, rmv_flgs=False, save_plt=True)
                    ac_plot.plt_time_mlty(info, out_dir=save_output, rmv_flgs=False, save_plt=True, hdrs=calc_index)
            else: pass

    if n_files_t != total_files:
        print()
        print("*** ERROR: Number of ACTIN calls different than number of files.")
        print("n_files_t:", n_files_t)
        print("total_files:", total_files)

    elapsed_time = (time.time() - start_time)/60

    # Summary:
    print("\n---------------------------------")
    print("Fractional pixels:\t{}".format(frac))
    print("Files analysed:\t\t{}".format(total_files))
    print("Save output:\t\t{}".format(save_output))
    print("Elapsed time:\t\t{:.4f} min".format(elapsed_time))

    return


def get_config():
    """
    Check for existence of ACTIN folder and config file and creates them if not present. Returns the path to the config file.
    """
    cfg_dir = appdirs.user_config_dir('ACTIN')
    if not os.path.exists(cfg_dir):
        os.makedirs(cfg_dir)
    cfg_file = os.path.join(cfg_dir, 'config_lines.txt')
    if not os.path.isfile(cfg_file):
        create_user_config(cfg_file)

    return cfg_file


def create_user_config(cfg_file):
    """
    Create the user's config file
    """
    from shutil import copyfile ###
    src = pkg_resources.resource_stream(__name__, 'config_lines.txt')
    copyfile(src.name, cfg_file)



def main():
    """
    Main function, call actin function with arguments from terminal.
    """

    # initiate the parser
    parser = argparse.ArgumentParser()

    # add short and long argument
    parser.add_argument('--files', '-f', help='Read file(s)', nargs='+')

    parser.add_argument('--calc_index', '-i', help="Index id to calculate as designated by 'ind_id' in config_index.txt.", nargs='+', default=None)

    parser.add_argument('--rv_in', '-rv', help="RV value to calibrate wavelength. If False (default) try to read RV from CCF file.", nargs='+', default=None, type=float)

    parser.add_argument('--config_file', '-cf', help='Path to config_file, or False (default) read config file from standard directory.', default=None)

    parser.add_argument('--save_output', '-s', help='Path to output directory of data table, or False (default).', default=False)

    parser.add_argument('--ln_plts', '-lp', help="Path to directory to save line plots. If 'same' saves line plots to same directory of data output. If 'show' only shows the plots. If 'False' (default) does not save or show line plots", default=False)

    parser.add_argument('--obj_name', '-obj', help='Give target a name that overides the one from the fits files.', default=None)

    parser.add_argument('--targ_list', '-tl', help='Give a list of stars to select from fits files.', nargs='+', default=None)

    parser.add_argument('--del_out', '-del', help='Delete output data file if True.', default=False, type=lambda x: (str(x).lower() == 'true'))

    parser.add_argument('--test', '-t', help='Tests actin using the provided fits files in the "test_files" directory. Options are "e2ds", "s1d", and "adp"', default=False)

    parser.add_argument('--frac', '-frc', help='Turns fractional pixel on (True, default) or off (False).', default=True, type=lambda x: (str(x).lower() == 'true'))

    parser.add_argument('--save_plots', '-sp', help="If True saves time-series and multi-plots to same directory as 'save_output'.", default=False, type=lambda x: (str(x).lower() == 'true'))


    # read arguments from the command lines
    args = parser.parse_args()

    actin(files       = args.files,
          calc_index  = args.calc_index,
          rv_in       = args.rv_in,
          config_file = args.config_file,
          save_output = args.save_output,
          ln_plts     = args.ln_plts,
          obj_name    = args.obj_name,
          targ_list   = args.targ_list,
          del_out     = args.del_out,
          test        = args.test,
          frac        = args.frac,
          save_plots  = args.save_plots)

if __name__ == "__main__":
    ac_set.preamble(version_file, verbose=True)
    main()

#!/usr/bin/env python # compatibility with python 2/3: # Directory of this file # Global variables #import ac_settings as ac_set # Global variables # initiate global variables: # Configuration file: # Version file: # Print preamble: Runs ACTIN for one fits file.     Accepts files of types: 'S2D', 'S1D', 'e2ds', 's1d', 's1d_*_rv', 'ADP', and 'rdb'.     Recognizes fits files from HARPS, HARPS-N and ESPRESSO instruments. # Check if file is from known instrument # Checking if object in targ_list is the same as the object in fits file # Read config file and retrieve lines information # Read data from file # Check output file for duplicates # Check selected lines for spectral range and orders # Calculate flux in the required lines # Calculate chosen indices # Write output to rdb file in "out_dir"/"obj" Runs 'actin_file' function for one or multiple fits files, for one or multiple stars.     Accepts fits files from HARPS, HARPS-N, and ESPRESSO instruments.     Accepts files of types: 'S1D', 'S2D', 'e2ds', 's1d', 's1d_*_rv', 'ADP', and 'rdb'. # Get config file from installation or input # test values can be 'S1D', 'S2D', 'e2ds', 's1d', 'adp', or 'rdb' # this needs to have before anything that uses 'files' # Make lists to be iterated below ### added float to use as module # Check if files exist # Remove output file #ac_tools.remove_output(files, save_output, targ_list) # Option to make line plots directory the same as the data output dir # Organize files by path to star and file type # star directories # file types # files organized by dir and file type # Run actin file # POST-PROCESSING: # Dictionaries for each file type # Save log and line info files # Save time-series plots # Summary: Check for existence of ACTIN folder and config file and creates them if not present. Returns the path to the config file. Create the user's config file ### Main function, call actin function with arguments from terminal. # initiate the parser # add short and long argument # read arguments from the command lines