diff --git a/bin/isisnet2socet b/bin/isisnet2socet
index 5291f162b774e2b0d743ea44eca00c6f0a987159..263c82d24ae7bc4a2891a7c55bca8871bcab96ce 100644
--- a/bin/isisnet2socet
+++ b/bin/isisnet2socet
@@ -1,25 +1,24 @@
#!/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])
diff --git a/bin/socetnet2isis b/bin/socetnet2isis
index 53cef03df1d73c4b711bb958125f6e57b109e906..1bbef96ec726cc008b829502d7b84d76748cc6cd 100644
--- a/bin/socetnet2isis
+++ b/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.')
@@ -26,10 +27,14 @@ 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):
+ if( args.outpath ):
outpath = args.outpath
else:
outpath = os.path.split(at_file)[0]
@@ -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)
diff --git a/plio/spatial/transformations.py b/plio/spatial/transformations.py
index b185a9d8f60e4fb5e1aacf8e2639e1a6f5d7b7b5..a624f3f4a4a527b0602680d6b02b2cd10484c2a5 100644
--- a/plio/spatial/transformations.py
+++ b/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
-------
@@ -467,12 +441,12 @@ 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')
- new_line = record['l.'] - (int(line_size/2.0)) - 1
- new_sample = record['s.'] - (int(sample_size/2.0)) - 1
+ new_line = record['l.'] - (int(line_size / 2.0)) - 1
+ new_sample = record['s.'] - (int(sample_size / 2.0)) - 1
return new_line, new_sample
diff --git a/plio/utils/utils.py b/plio/utils/utils.py
index 2215f7558cafda549fd94ecc4013fcbfadec75e5..4ef547489d0fe016d85a6697bf202bde08b01f1b 100644
--- a/plio/utils/utils.py
+++ b/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