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.

bin/isisnet2socet

 #!/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

@@ -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

@@ -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

@@ -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