Added file to read Jonathan's mock cubes

src/data/mocks_create/florez_cubes.py

@@ -0,0 +1,279 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# Victor Calderon
+# Created      : 2018-06-27
+# Last Modified: 2018-06-27
+# Vanderbilt University
+from __future__ import absolute_import, division, print_function 
+__author__     = ['Victor Calderon']
+__copyright__  = ["Copyright 2018 Victor Calderon, "]
+__email__      = ['victor.calderon@vanderbilt.edu']
+__maintainer__ = ['Victor Calderon']
+"""
+Script to turn specific simulation data into Pandas Dataframes
+"""
+# Importing Modules
+from cosmo_utils       import mock_catalogues as cm
+from cosmo_utils       import utils           as cu
+from cosmo_utils.utils import file_utils      as cfutils
+from cosmo_utils.utils import file_readers    as cfreaders
+from cosmo_utils.utils import work_paths      as cwpaths
+from cosmo_utils.utils import stats_funcs     as cstats
+from cosmo_utils.utils import geometry        as cgeom
+from cosmo_utils.mock_catalogues import catls_utils as cmcu
+
+import numpy as num
+import math
+import os
+import sys
+import pandas as pd
+import pickle
+import matplotlib
+matplotlib.use( 'Agg' )
+import matplotlib.pyplot as plt
+import matplotlib.ticker as ticker
+plt.rc('text', usetex=True)
+import seaborn as sns
+#sns.set()
+from progressbar import (Bar, ETA, FileTransferSpeed, Percentage, ProgressBar,
+                        ReverseBar, RotatingMarker)
+from tqdm import tqdm
+
+# Extra-modules
+import argparse
+from argparse import ArgumentParser
+from argparse import HelpFormatter
+from operator import attrgetter
+from tqdm import tqdm
+
+## Functions
+class SortingHelpFormatter(HelpFormatter):
+    def add_arguments(self, actions):
+        """
+        Modifier for `argparse` help parameters, that sorts them alphabetically
+        """
+        actions = sorted(actions, key=attrgetter('option_strings'))
+        super(SortingHelpFormatter, self).add_arguments(actions)
+
+def _str2bool(v):
+    if v.lower() in ('yes', 'true', 't', 'y', '1'):
+        return True
+    elif v.lower() in ('no', 'false', 'f', 'n', '0'):
+        return False
+    else:
+        raise argparse.ArgumentTypeError('Boolean value expected.')
+
+def _check_pos_val(val, val_min=0):
+    """
+    Checks if value is larger than `val_min`
+
+    Parameters
+    ----------
+    val: int or float
+        value to be evaluated by `val_min`
+
+    val_min: float or int, optional (default = 0)
+        minimum value that `val` can be
+
+    Returns
+    -------
+    ival: float
+        value if `val` is larger than `val_min`
+
+    Raises
+    -------
+    ArgumentTypeError: Raised if `val` is NOT larger than `val_min`
+    """
+    ival = float(val)
+    if ival <= val_min:
+        msg  = '`{0}` is an invalid input!'.format(ival)
+        msg += '`val` must be larger than `{0}`!!'.format(val_min)
+        raise argparse.ArgumentTypeError(msg)
+
+    return ival
+
+def get_parser():
+    """
+    Get parser object for `eco_mocks_create.py` script.
+
+    Returns
+    -------
+    args: 
+        input arguments to the script
+    """
+    ## Define parser object
+    description_msg = 'Description of Script'
+    parser = ArgumentParser(description=description_msg,
+                            formatter_class=SortingHelpFormatter,)
+    ## 
+    parser.add_argument('--version', action='version', version='%(prog)s 1.0')
+
+    ## Program message
+    parser.add_argument('-progmsg',
+                        dest='Prog_msg',
+                        help='Program message to use throught the script',
+                        type=str,
+                        default=cfutils.Program_Msg(__file__))
+    ## Parsing Objects
+    args = parser.parse_args()
+
+    return args
+
+def param_vals_test(param_dict):
+    """
+    Checks if values are consistent with each other.
+
+    Parameters
+    -----------
+    param_dict: python dictionary
+        dictionary with `project` variables
+
+    Raises
+    -----------
+    ValueError: Error
+        This function raises a `ValueError` error if one or more of the 
+        required criteria are not met
+    """
+    ##
+    ## This is where the tests for `param_dict` input parameters go.
+
+def is_tool(name):
+    """Check whether `name` is on PATH and marked as executable."""
+
+    # from whichcraft import which
+    from shutil import which
+
+    return which(name) is not None
+
+def add_to_dict(param_dict):
+    """
+    Aggregates extra variables to dictionary
+
+    Parameters
+    ----------
+    param_dict: python dictionary
+        dictionary with input parameters and values
+
+    Returns
+    ----------
+    param_dict: python dictionary
+        dictionary with old and new values added
+    """
+    # This is where you define `extra` parameters for adding to `param_dict`.
+
+    return param_dict
+
+def directory_skeleton(param_dict, proj_dict):
+    """
+    Creates the directory skeleton for the current project
+
+    Parameters
+    ----------
+    param_dict: python dictionary
+        dictionary with `project` variables
+
+    proj_dict: python dictionary
+        dictionary with info of the project that uses the
+        `Data Science` Cookiecutter template.
+
+    Returns
+    ---------
+    proj_dict: python dictionary
+        Dictionary with current and new paths to project directories
+    """
+    file_msg = param_dict['Prog_msg']
+    ## Path to the simulation cubes to analyze
+    sim_dir = os.path.join('/fs1/caldervf/CODES/vandy_group_statistics2',
+                            'RESOLVE_Mocks_Cube_Color_Age',
+                            'With_Weights',
+                            'New_Mocks')
+    # Checking that folder exists
+    if not (os.path.exists(sim_dir)):
+        msg = '{0} `sim_dir` ({1}) does not exist!'.format(file_msg, sim_dir)
+        raise FileNotFoundError(msg)
+    # Finding combination of the directory
+    simfile = os.path.join(sim_dir,
+        'Mbaryon_9.0_Vpeak_0.2_u-r_Acc_Rate_100Myr_0.6_130.0.hdf5')
+    # Check that file exists
+    if not (os.path.exists(simfile)):
+        msg = '{0} `simfile` ({1}) does not exist!'.format(file_msg, simfile)
+        raise FileNotFoundError(msg)
+    #
+    # Saving to dictionary
+    proj_dict['sim_dir'] = sim_dir
+    proj_dict['simfile'] = simfile
+
+    return proj_dict
+
+## -------------------- Data Extraction -------------------- ##
+def simfile_data_extraction(param_dict, proj_dict):
+    """
+    Extracts the data from the simulation file and converts it to
+    a Pandas DataFrame.
+
+    Parameters
+    -----------
+    param_dict : `dict`
+        Dictionary with input parameters and values
+
+    proj_dict : `dict`
+        Dictionary with info of the project that uses the
+        `Data Science` Cookiecutter template.
+
+    Returns
+    -----------
+    sim_pd : `pd.DataFrame`
+        DataFrame containing the necessary information of `simfile`.
+    """
+    file_msg = param_dict['Prog_msg']
+    # Constatns
+    cens = int(1)
+    sats = int(0)
+    # Columns to be extracted
+    sim_cols = ['Mbaryon', 'Vpeak', 'mvir', 'Acc_Rate_100Myr', 'u-r',
+                'FSMGR', 'pid', 'id', 'upid']
+    # Reading in filename and converting it to Pandas DataFrame
+    sim_pd_tot = cfreaders.read_hdf5_file_to_pandas_DF(proj_dict['simfile'])
+    # Only selecting certaing columns
+    sim_pd = sim_pd_tot.loc[:, sim_cols]
+    #
+    # Figuring out host halo's mass
+    halo_id = [[] for x in range(len(sim_pd))]
+
+## -------------------- Main Function -------------------- ##
+
+def main(args):
+    """
+    Script to turn specific simulation data into Pandas Dataframes
+    """
+    ## Reading all elements and converting to python dictionary
+    param_dict = vars(args)
+    ## Checking for correct input
+    param_vals_test(param_dict)
+    ## Adding extra variables
+    param_dict = add_to_dict(param_dict)
+    ## Program message
+    Prog_msg = param_dict['Prog_msg']
+    ##
+    ## Creating Folder Structure
+    # proj_dict  = directory_skeleton(param_dict, cwpaths.cookiecutter_paths(__file__))
+    proj_dict  = directory_skeleton(param_dict, cwpaths.cookiecutter_paths('./'))
+    ##
+    ## Printing out project variables
+    print('\n'+50*'='+'\n')
+    for key, key_val in sorted(param_dict.items()):
+        if key !='Prog_msg':
+            print('{0} `{1}`: {2}'.format(Prog_msg, key, key_val))
+    print('\n'+50*'='+'\n')
+    #
+    # Extracting info from `simfile`
+    sim_pd = 
+
+
+# Main function
+if __name__=='__main__':
+    ## Input arguments
+    args = get_parser()
+    # Main Function
+    main(args)