Commit 398f1178 authored by acpaquette's avatar acpaquette Committed by jlaura
Browse files

Socet clean up (#58) 

* Small updates to get the scripts working.

* Fixed pradius calculations, and made some small changes.

* Removed coord transforms and made body_fix func more generic.

* Updated version.

* Updated reproj doc string.

* General refactor to socet scripts and clean up. Simplfied input for both scripts.
parent 0017d486

bin/isisnet2socet

+8 −12
Original line number Diff line number Diff line 
#!/usr/bin/env python

import argparse

import os

import math

import argparse



import pandas as pd



from plio.io.io_bae import save_gpf, save_ipf

from plio.spatial.transformations import apply_isis_transformations

import plio.io.io_controlnetwork as cn

import plio.io.isis_serial_number as sn

from plio.spatial.transformations import apply_isis_transformations

from plio.utils.utils import split_all_ext



def parse_args():

    parser = argparse.ArgumentParser()



    # Add args here

    parser.add_argument('cnet_file', help='Path to an isis control network.')

    parser.add_argument('e_radius', type=float, help='The semimajor radius of a given target.')

    parser.add_argument('eccentricity', type=float, help='The eccentricity of a given target.')

    parser.add_argument('cub_path', help='Path to the cub files associated with a control network.')

    parser.add_argument('cub_extension', help='Extension for all cubes.')

    parser.add_argument('cub_list', help='Path to a list file of all cubes being used')

    parser.add_argument('cub_list', help='Path to a list file of all cubes being used. This \

                                                                 includes file paths an extnsions.')

    parser.add_argument('out_gpf', help='Path to save location of gpf file and new ipf files.')

    parser.add_argument('--adjusted', help='Flag for saving apriori values or adjusted values',

                                      default=False, required = False)
@@ -34,9 +33,6 @@ def main(args): 
    e_radius = args.e_radius

    p_radius = e_radius * math.sqrt((1 - (args.eccentricity ** 2)))



    cub_path = args.cub_path

    extension = args.cub_extension



    with open(args.cub_list, 'r') as f:

        lines = f.readlines()

        cub_list = [cub.replace('\n', '') for cub in lines]
@@ -46,10 +42,10 @@ def main(args): 
    adjusted_flag = args.adjusted



    # Create cub dict to map ipf to cub

    cub_dict = {i: i + extension for i in cub_list}

    cub_dict = {split_all_ext(os.path.split(i)[1]): i for i in cub_list}



    # Create serial dict to match serial to ipf

    serial_dict = {sn.generate_serial_number(os.path.join(cub_path, i + extension)): i for i in cub_list}

    serial_dict = {sn.generate_serial_number(i): split_all_ext(os.path.split(i)[-1]) for i in cub_list}



    # Remove duplicate columns

    # There are better ways to do this but pandas was not having it
@@ -82,7 +78,7 @@ def main(args): 


    df.rename(columns = column_map, inplace=True)



    apply_isis_transformations(df, e_radius, p_radius, serial_dict, extension, cub_path)

    apply_isis_transformations(df, e_radius, p_radius, serial_dict, cub_dict)



    # Save the ipf(s)

    save_ipf(df, os.path.split(out_gpf)[0])

bin/socetnet2isis

+15 −11
Original line number Diff line number Diff line
@@ -4,19 +4,20 @@ import sys 
import argparse

import warnings



import pandas as pd



from plio.io.io_bae import read_atf, read_gpf, read_ipf

from plio.spatial.transformations import apply_socet_transformations, serial_numbers

import plio.io.io_controlnetwork as cn



import pandas as pd

import plio.io.isis_serial_number as sn

from plio.spatial.transformations import apply_socet_transformations

from plio.utils.utils import split_all_ext



def parse_args():

    parser = argparse.ArgumentParser()



    # Add args here

    parser.add_argument('at_file', help='Path to the .atf file for a project.')

    parser.add_argument('cub_file_path', help='Path to cube files related to ipf files.')

    parser.add_argument('extension', help='Extension for all cubes being used.')

    parser.add_argument('cub_list', help='Path to a list file containing paths to the associated\

                                                                 Isis cubes.')

    parser.add_argument('target_name', help='Name of the target body used in the control net')

    parser.add_argument('--outpath', help='Directory for the control network to be output to.')
@@ -26,8 +27,12 @@ def parse_args(): 
def main(args):

    # Setup the at_file, path to cubes, and control network out path

    at_file = args.at_file



    with open(args.cub_list, 'r') as f:

        lines = f.readlines()

        cub_list = [cub.replace('\n', '') for cub in lines]



    cnet_out = os.path.split(os.path.splitext(at_file)[0])[1]

    cub_path = args.cub_file_path



    if( args.outpath ):

        outpath = args.outpath
@@ -72,9 +77,8 @@ def main(args): 
    # Rename the columns using the column remap above

    socet_df.rename(columns = column_map, inplace=True)



    # Build an image and serial dict assuming the cubes will be named as the IPFs are

    image_dict = {i: i + args.extension for i in pd.unique(socet_df['ipf_file'])}

    serial_dict = serial_numbers(image_dict, cub_path)

    # Build a serial dict assuming the cubes will be named as the IPFs are

    serial_dict = {split_all_ext(os.path.split(i)[-1]): sn.generate_serial_number(i) for i in cub_list}



    # creates the control network

    cn.to_isis(os.path.join(outpath, cnet_out + '.net'), socet_df, serial_dict, targetname = args.target_name)

plio/spatial/transformations.py

+8 −34
Original line number Diff line number Diff line
@@ -218,7 +218,7 @@ def stat_toggle(record): 
    else:

        return False



def apply_isis_transformations(df, eRadius, pRadius, serial_dict, extension, cub_path):

def apply_isis_transformations(df, eRadius, pRadius, serial_dict, cub_dict):

    """

    Takes a atf dictionary and a socet dataframe and applies the necessary

    transformations to convert that dataframe into a isis compatible
@@ -261,8 +261,7 @@ def apply_isis_transformations(df, eRadius, pRadius, serial_dict, extension, cub 
    df['known'] = df.apply(reverse_known, axis = 1)

    df['ipf_file'] = df['serialnumber'].apply(lambda serial_number: serial_dict[serial_number])

    df['l.'], df['s.'] = zip(*df.apply(fix_sample_line, serial_dict = serial_dict,

                                       extension = extension,

                                       cub_path = cub_path, axis = 1))

                                       cub_dict = cub_dict, axis = 1))



    # Add dummy for generic value setting

    x_dummy = lambda x: np.full(len(df), x)
@@ -313,28 +312,6 @@ def apply_socet_transformations(atf_dict, df): 
    df['aprioriCovar'] = df.apply(compute_cov_matrix, semimajor_axis = eRadius, axis=1)

    df['stat'] = df.apply(stat_toggle, axis=1)



def serial_numbers(image_dict, path):

    """

    Creates a dict of serial numbers with the cub being the key



    Parameters

    ----------

    images : list



    path : str



    extension : str



    Returns

    -------

    serial_dict : dict

    """

    serial_dict = dict()



    for key in image_dict:

        serial_dict[key] = sn.generate_serial_number(os.path.join(path, image_dict[key]))

    return serial_dict



# TODO: Does isis cnet need a convariance matrix for sigmas? Even with a static matrix of 1,1,1,1

def compute_sigma_covariance_matrix(lat, lon, rad, latsigma, lonsigma, radsigma, semimajor_axis):
@@ -438,7 +415,7 @@ def reverse_known(record): 
    elif record_type == 1 or record_type == 3 or record_type == 4:

        return 3



def fix_sample_line(record, serial_dict, extension, cub_path):

def fix_sample_line(record, serial_dict, cub_dict):

    """

    Extracts the sample, line data from a cube and computes deviation from the

    center of the image
@@ -451,11 +428,8 @@ def fix_sample_line(record, serial_dict, extension, cub_path): 
    serial_dict : dict

                  Maps serial numbers to images



    extension : str

                Extension for cube being looked at



    cub_path : str

               Path to a given cube being looked at

    cub_dict : dict

                     Maps basic cub names to their assocated absoluate path cubs



    Returns

    -------
@@ -467,7 +441,7 @@ def fix_sample_line(record, serial_dict, extension, cub_path): 


    """

    # Cube location to load

    cube = pvl.load(os.path.join(cub_path, serial_dict[record['serialnumber']] + extension))

    cube = pvl.load(cub_dict[serial_dict[record['serialnumber']]])

    line_size = find_in_dict(cube, 'Lines')

    sample_size = find_in_dict(cube, 'Samples')

plio/utils/utils.py

+21 −0
Original line number Diff line number Diff line
@@ -181,3 +181,24 @@ def lookup(df, lookupfile=None, lookupdf=None, sep=',', skiprows=1, left_on='scl 
    # combine the df and the new metadata

    df = pd.concat([metadata, df], axis=1)

    return df



def split_all_ext(path):

    """

    General function for removeing all potential extensions from a file.



    Parameters

    ----------

    path : str

              Path or file name with potential extension



    Returns

    -------

    base : str

               Path or file name with all potnetial extensions removed

    """

    base, ext = os.path.splitext(path)



    while len(ext) is not 0:

        base, ext = os.path.splitext(base)



    return base