diff --git a/bin/Socetnet2ISIS.py b/bin/Socetnet2ISIS.py
deleted file mode 100644
index 79765170ee5246e52d1f60a9634ad51b68ae01b8..0000000000000000000000000000000000000000
--- a/bin/Socetnet2ISIS.py
+++ /dev/null
@@ -1,49 +0,0 @@
-import os
-import numpy as np
-
-# Reads a .atf file and outputs all of the
-# .ipf, .gpf, .sup, .prj, and path to locate the
-# .apf file (should be the same as all others)
-def read_atf(atf_file):
- with open(atf_file) as f:
-
- files = []
- ipf = []
- sup = []
- files_dict = []
-
- # Grabs every PRJ, GPF, SUP, and IPF image from the ATF file
- for line in f:
- if line[-4:-1] == 'prj' or line[-4:-1] == 'gpf' or line[-4:-1] == 'sup' or line[-4:-1] == 'ipf' or line[-4:-1] == 'atf':
- files.append(line)
-
- files = np.array(files)
-
- # Creates appropriate arrays for certain files in the right format
- for file in files:
- file = file.strip()
- file = file.split(' ')
-
- # Grabs all the IPF files
- if file[1].endswith('.ipf'):
- ipf.append(file[1])
-
- # Grabs all the SUP files
- if file[1].endswith('.sup'):
- sup.append(file[1])
-
- files_dict.append(file)
-
- # Creates a dict out of file lists for GPF, PRJ, IPF, and ATF
- files_dict = (dict(files_dict))
-
- # Sets the value of IMAGE_IPF to all IPF images
- files_dict['IMAGE_IPF'] = ipf
-
- # Sets the value of IMAGE_SUP to all SUP images
- files_dict['IMAGE_SUP'] = sup
-
- # Sets the value of PATH to the path of the ATF file
- files_dict['PATH'] = os.path.dirname(os.path.abspath(atf_file))
-
- return files_dict
diff --git a/bin/socet2isis b/bin/socet2isis
index 44255aec300c8ad9f4aed798258a8a9cf8fb89c6..2fe05808f4f518ef9f7586cf31bd3cfb57c5cb22 100644
--- a/bin/socet2isis
+++ b/bin/socet2isis
@@ -1,15 +1,92 @@
#!/usr/bin/env python
import argparse
+import os
+import sys
+import warnings
+import csv
+import numpy as np
+
+from plio.examples import get_path
+from plio.io.io_bae import read_atf, read_gpf, read_ipf
+from plio.spatial.transformations import *
+import plio.io.io_controlnetwork as cn
+
+import pandas as pd
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('cub_ipf_map', help='Path to map file for all ipfs and cubes.')
+ parser.add_argument('--outpath', help='Directory for the control network to be output to.',
+ required = False)
return parser.parse_args()
def main(args):
- print('Getting some work done')
+ # Setup the at_file, path to cubes, and control network out path
+ at_file = args.at_file
+ cnet_out = os.path.split(os.path.splitext(at_file)[0])[1]
+ cub_path = args.cub_file_path
+
+ if(args.outpath):
+ outpath = args.outpath
+ else:
+ outpath = os.path.split(at_file)[0]
+
+ with open(args.cub_ipf_map) as cub_ipf_map:
+ reader = csv.reader(cub_ipf_map, delimiter = ',')
+ image_dict = dict([(row[0], row[1]) for row in reader])
+
+ # Read in and setup the atf dict of information
+ atf_dict = read_atf(at_file)
+
+ # Get the gpf and ipf files using atf dict
+ gpf_file = os.path.join(atf_dict['PATH'], atf_dict['GP_FILE']);
+ ipf_list = [os.path.join(atf_dict['PATH'], i) for i in atf_dict['IMAGE_IPF']]
+
+ # Read in the gpf file and ipf file(s) into seperate dataframes
+ gpf_df = read_gpf(gpf_file)
+ ipf_df = read_ipf(ipf_list)
+
+ # Check for differences between point ids using each dataframes
+ # point ids as a reference
+ gpf_pt_idx = pd.Index(pd.unique(gpf_df['point_id']))
+ ipf_pt_idx = pd.Index(pd.unique(ipf_df['pt_id']))
+
+ point_diff = ipf_pt_idx.difference(gpf_pt_idx)
+
+ if len(point_diff) != 0:
+ warnings.warn("The following points found in ipf files missing from gpf file: " +
+ "\n\n{}\n\n".format("\n".join(point_diff)) +
+ "Continuing, but these points will be missing from the control " +
+ "network.", stacklevel=3)
+
+ # Merge the two dataframes on their point id columns
+ socet_df = ipf_df.merge(gpf_df, left_on='pt_id', right_on='point_id')
+
+ # Apply the transformations
+ apply_transformations(atf_dict, socet_df)
+
+ # Define column remap for socet dataframe
+ column_remap = {'l.': 'y', 's.': 'x',
+ 'res_l': 'LineResidual', 'res_s': 'SampleResidual', 'known': 'Type',
+ 'lat_Y_North': 'AprioriY', 'long_X_East': 'AprioriX', 'ht': 'AprioriZ',
+ 'sig0': 'AprioriLatitudeSigma', 'sig1': 'AprioriLongitudeSigma',
+ 'sig2': 'AprioriRadiusSigma'}
+
+ # Rename the columns using the column remap above
+ socet_df.rename(columns = column_remap, inplace=True)
+
+ images = pd.unique(socet_df['ipf_file'])
+
+ serial_dict = serial_numbers(image_dict, cub_path)
+
+ # creates the control network
+ cn.to_isis(os.path.join(outpath, cnet_out + '.net'), socet_df, serial_dict)
if __name__ == '__main__':
- main(parse_args())
\ No newline at end of file
+ main(parse_args())
diff --git a/notebooks/Socet2ISIS.ipynb b/notebooks/Socet2ISIS.ipynb
index 1d7681a240afaf6e83d53f2321d4150482ce5fd5..f9ff8e2dd784c0c36eca6a96d8133d847e531657 100644
--- a/notebooks/Socet2ISIS.ipynb
+++ b/notebooks/Socet2ISIS.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -26,7 +26,7 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -224,49 +224,44 @@
" return socet_df\n",
"\n",
"# creates a dict of serial numbers with the cub being the key\n",
- "def serial_numbers(images, path, extension):\n",
+ "def serial_numbers(image_dict, path):\n",
" serial_dict = dict()\n",
- " \n",
- " for image in images:\n",
- " snum = sn.generate_serial_number(os.path.join(path, image + extension))\n",
+ "\n",
+ " for key in image_dict:\n",
+ " snum = sn.generate_serial_number(os.path.join(path, image_dict[key]))\n",
" snum = snum.replace('Mars_Reconnaissance_Orbiter', 'MRO')\n",
- " serial_dict[image] = snum\n",
+ " serial_dict[key] = snum\n",
" return serial_dict"
]
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": null,
"metadata": {
"scrolled": false
},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/Users/adampaquette/anaconda/envs/pysat/lib/python3.6/site-packages/ipykernel_launcher.py:173: UserWarning: The following points found in ipf files missing from gpf file: \n",
- "\n",
- "['P03_002226_1895_XI_09N203W_15', 'P03_002226_1895_XI_09N203W_16', 'P03_002226_1895_XI_09N203W_17', 'P03_002226_1895_XI_09N203W_18', 'P03_002226_1895_XI_09N203W_19', 'P03_002226_1895_XI_09N203W_20', 'P03_002226_1895_XI_09N203W_21', 'P03_002226_1895_XI_09N203W_22', 'P03_002226_1895_XI_09N203W_24', 'P03_002226_1895_XI_09N203W_26', 'P03_002226_1895_XI_09N203W_30', 'P03_002226_1895_XI_09N203W_31', 'P03_002226_1895_XI_09N203W_32', 'P03_002226_1895_XI_09N203W_34', 'P03_002226_1895_XI_09N203W_36', 'P03_002226_1895_XI_09N203W_37', 'P03_002226_1895_XI_09N203W_44', 'P03_002226_1895_XI_09N203W_48', 'P03_002226_1895_XI_09N203W_49', 'P03_002226_1895_XI_09N203W_56', 'P03_002226_1895_XI_09N203W_57', 'P03_002226_1895_XI_09N203W_61', 'P03_002226_1895_XI_09N203W_62', 'P03_002226_1895_XI_09N203W_63', 'P03_002226_1895_XI_09N203W_65', 'P19_008344_1894_XN_09N203W_4', 'P20_008845_1894_XN_09N203W_15']. \n",
- "\n",
- "Continuing, but these points will be missing from the control network\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Setup stuffs for the cub information namely the path and extension\n",
"path = '/Volumes/Blueman/'\n",
- "extension = '.lev1.cub'\n",
- "prj_file = get_path('CTX_Athabasca_Middle_step0.atf')\n",
+ "atf_file = get_path('CTX_Athabasca_Middle_step0.atf')\n",
+ "\n",
+ "image_dict = {'P01_001540_1889_XI_08N204W' : 'P01_001540_1889_XI_08N204W.lev1.cub',\n",
+ " 'P01_001606_1897_XI_09N203W' : 'P01_001606_1897_XI_09N203W.lev1.cub',\n",
+ " 'P02_001804_1889_XI_08N204W' : 'P02_001804_1889_XI_08N204W.lev1.cub',\n",
+ " 'P03_002226_1895_XI_09N203W' : 'P03_002226_1895_XI_09N203W.lev1.cub',\n",
+ " 'P03_002371_1888_XI_08N204W' : 'P03_002371_1888_XI_08N204W.lev1.cub',\n",
+ " 'P19_008344_1894_XN_09N203W' : 'P19_008344_1894_XN_09N203W.lev1.cub',\n",
+ " 'P20_008845_1894_XN_09N203W' : 'P20_008845_1894_XN_09N203W.lev1.cub'}\n",
"\n",
- "socet_df = socet2isis(prj_file)\n",
+ "socet_df = socet2isis(atf_file)\n",
"\n",
"images = pd.unique(socet_df['ipf_file'])\n",
"\n",
- "serial_dict = serial_numbers(images, path, extension)\n",
+ "serial_dict = serial_numbers(image_dict, path)\n",
"\n",
"# creates the control network\n",
- "cn.to_isis('/Volumes/Blueman/cn.net', socet_df, serial_dict)"
+ "cn.to_isis('/Volumes/Blueman/banana.net', socet_df, serial_dict)"
]
},
{
diff --git a/plio/examples/SocetSet/cub_map.csv b/plio/examples/SocetSet/cub_map.csv
new file mode 100644
index 0000000000000000000000000000000000000000..cca0f2c17b832f4df5ac001bafde185ca679cdd7
--- /dev/null
+++ b/plio/examples/SocetSet/cub_map.csv
@@ -0,0 +1,7 @@
+P01_001540_1889_XI_08N204W,P01_001540_1889_XI_08N204W.lev1.cub
+P01_001606_1897_XI_09N203W,P01_001606_1897_XI_09N203W.lev1.cub
+P02_001804_1889_XI_08N204W,P02_001804_1889_XI_08N204W.lev1.cub
+P03_002226_1895_XI_09N203W,P03_002226_1895_XI_09N203W.lev1.cub
+P03_002371_1888_XI_08N204W,P03_002371_1888_XI_08N204W.lev1.cub
+P19_008344_1894_XN_09N203W,P19_008344_1894_XN_09N203W.lev1.cub
+P20_008845_1894_XN_09N203W,P20_008845_1894_XN_09N203W.lev1.cub
diff --git a/plio/io/io_bae.py b/plio/io/io_bae.py
index 37e5abc4345c77c09d9dfecffef6abfc2ecd6df0..2810a8e19e91a8c9ad2472b2adb3d92783ff1faf 100644
--- a/plio/io/io_bae.py
+++ b/plio/io/io_bae.py
@@ -271,3 +271,63 @@ def save_gpf(df, output_file):
outGPF.close()
return
+
+def read_atf(atf_file):
+ """
+ Reads a .atf file and outputs all of the
+ .ipf, .gpf, .sup, .prj, and path to locate the
+ .apf file (should be the same as all others)
+
+ Parameters
+ ----------
+ atf_file : str
+ Full path to a socet atf file
+
+ Returns
+ -------
+ files_dict : dict
+ Dict of files and data associated with a socet
+ project
+ """
+ with open(atf_file) as f:
+
+ files = []
+ ipf = []
+ sup = []
+ files_dict = []
+
+ # Grabs every PRJ, GPF, SUP, and IPF image from the ATF file
+ for line in f:
+ if line[-4:-1] == 'prj' or line[-4:-1] == 'gpf' or line[-4:-1] == 'sup' or line[-4:-1] == 'ipf' or line[-4:-1] == 'atf':
+ files.append(line)
+
+ files = np.array(files)
+
+ # Creates appropriate arrays for certain files in the right format
+ for file in files:
+ file = file.strip()
+ file = file.split(' ')
+
+ # Grabs all the IPF files
+ if file[1].endswith('.ipf'):
+ ipf.append(file[1])
+
+ # Grabs all the SUP files
+ if file[1].endswith('.sup'):
+ sup.append(file[1])
+
+ files_dict.append(file)
+
+ # Creates a dict out of file lists for GPF, PRJ, IPF, and ATF
+ files_dict = (dict(files_dict))
+
+ # Sets the value of IMAGE_IPF to all IPF images
+ files_dict['IMAGE_IPF'] = ipf
+
+ # Sets the value of IMAGE_SUP to all SUP images
+ files_dict['IMAGE_SUP'] = sup
+
+ # Sets the value of PATH to the path of the ATF file
+ files_dict['PATH'] = os.path.dirname(os.path.abspath(atf_file))
+
+ return files_dict
diff --git a/plio/spatial/transformations.py b/plio/spatial/transformations.py
new file mode 100644
index 0000000000000000000000000000000000000000..efc4ad609424a1c88e4ca778370b647249655e4c
--- /dev/null
+++ b/plio/spatial/transformations.py
@@ -0,0 +1,292 @@
+import os
+import math
+import pyproj
+
+import plio.io.isis_serial_number as sn
+
+def line_sample_size(record, path):
+ """
+ Converts columns l. and s. to sample size, line size, and generates an
+ image index
+
+ Parameters
+ ----------
+ record : object
+ Pandas series object
+
+ path : str
+ Path to the associated sup files for a socet project
+
+ Returns
+ -------
+ : list
+ A list of sample_size, line_size, and img_index
+ """
+ with open(os.path.join(path, record['ipf_file'] + '.sup')) as f:
+ for i, line in enumerate(f):
+ if i == 2:
+ img_index = line.split('\\')
+ img_index = img_index[-1].strip()
+ img_index = img_index.split('.')[0]
+
+ if i == 3:
+ line_size = line.split(' ')
+ line_size = line_size[-1].strip()
+ assert int(line_size) > 0, "Line number {} from {} is a negative number: Invalid Data".format(line_size, record['ipf_file'])
+
+ if i == 4:
+ sample_size = line.split(' ')
+ sample_size = sample_size[-1].strip()
+ assert int(sample_size) > 0, "Sample number {} from {} is a negative number: Invalid Data".format(sample_size, record['ipf_file'])
+ break
+
+
+ line_size = int(line_size)/2.0 + record['l.'] + 1
+ sample_size = int(sample_size)/2.0 + record['s.'] + 1
+ return sample_size, line_size, img_index
+
+def known(record):
+ """
+ Converts the known field from a socet dataframe into the
+ isis point_type column
+
+ Parameters
+ ----------
+ record : object
+ Pandas series object
+
+ Returns
+ -------
+ : str
+ String representation of a known field
+ """
+ if record['known'] == 0:
+ return 'Free'
+
+ elif record['known'] == 1 or record['known'] == 2 or record['known'] == 3:
+ return 'Constrained'
+
+def to_360(num):
+ """
+ Transforms a given number into 0 - 360 space
+
+ Parameters
+ ----------
+ num : int
+ A given integer
+
+ Returns
+ -------
+ : int
+ num moduloed by 360
+ """
+ return num % 360
+
+def oc2og(dlat, dMajorRadius, dMinorRadius):
+ """
+ Ocentric to ographic latitudes
+
+ Parameters
+ ----------
+ dlat : float
+ Latitude to convert
+
+ dMajorRadius : float
+ Radius from the center of the body to the equater
+
+ dMinorRadius : float
+ Radius from the pole to the center of mass
+
+ Returns
+ -------
+ dlat : float
+ Converted latitude into ographic space
+ """
+ try:
+ dlat = math.radians(dlat)
+ dlat = math.atan(((dMajorRadius / dMinorRadius)**2) * (math.tan(dlat)))
+ dlat = math.degrees(dlat)
+ except:
+ print ("Error in oc2og conversion")
+ return dlat
+
+def og2oc(dlat, dMajorRadius, dMinorRadius):
+ """
+ Ographic to ocentric latitudes
+
+ Parameters
+ ----------
+ dlat : float
+ Latitude to convert
+
+ dMajorRadius : float
+ Radius from the center of the body to the equater
+
+ dMinorRadius : float
+ Radius from the pole to the center of mass
+
+ Returns
+ -------
+ dlat : float
+ Converted latitude into ocentric space
+ """
+ try:
+ dlat = math.radians(dlat)
+ dlat = math.atan((math.tan(dlat) / ((dMajorRadius / dMinorRadius)**2)))
+ dlat = math.degrees(dlat)
+ except:
+ print ("Error in og2oc conversion")
+ return dlat
+
+def get_axis(file):
+ """
+ Gets eRadius and pRadius from a .prj file
+
+ Parameters
+ ----------
+ file : str
+ file with path to a given socet project file
+
+ Returns
+ -------
+ : list
+ A list of the eRadius and pRadius of the project file
+ """
+ with open(file) as f:
+ from collections import defaultdict
+
+ files = defaultdict(list)
+
+ for line in f:
+
+ ext = line.strip().split(' ')
+ files[ext[0]].append(ext[-1])
+
+ eRadius = float(files['A_EARTH'][0])
+ pRadius = eRadius * (1 - float(files['E_EARTH'][0]))
+
+ return eRadius, pRadius
+
+def lat_ISIS_coord(record, semi_major, semi_minor):
+ """
+ Function to convert lat_Y_North to ISIS_lat
+
+ Parameters
+ ----------
+ record : object
+ Pandas series object
+
+ semi_major : float
+ Radius from the center of the body to the equater
+
+ semi_minor : float
+ Radius from the pole to the center of mass
+
+ Returns
+ -------
+ coord_360 : float
+ Converted latitude into ocentric space, and mapped
+ into 0 to 360
+ """
+ ocentric_coord = og2oc(record['lat_Y_North'], semi_major, semi_minor)
+ coord_360 = to_360(ocentric_coord)
+ return coord_360
+
+def lon_ISIS_coord(record, semi_major, semi_minor):
+ """
+ Function to convert long_X_East to ISIS_lon
+
+ Parameters
+ ----------
+ record : object
+ Pandas series object
+
+ semi_major : float
+ Radius from the center of the body to the equater
+
+ semi_minor : float
+ Radius from the pole to the center of mass
+
+ Returns
+ -------
+ coord_360 : float
+ Converted longitude into ocentric space, and mapped
+ into 0 to 360
+ """
+ ocentric_coord = og2oc(record['long_X_East'], semi_major, semi_minor)
+ coord_360 = to_360(ocentric_coord)
+ return coord_360
+
+def body_fix(record, semi_major, semi_minor):
+ """
+ Transforms latitude, longitude, and height of a socet point into
+ a body fixed point
+
+ Parameters
+ ----------
+ record : object
+ Pandas series object
+
+ semi_major : float
+ Radius from the center of the body to the equater
+
+ semi_minor : float
+ Radius from the pole to the center of mass
+
+ Returns
+ -------
+ : list
+ Body fixed lat, lon and height coordinates as lat, lon, ht
+
+ """
+ ecef = pyproj.Proj(proj='geocent', a=semi_major, b=semi_minor)
+ lla = pyproj.Proj(proj='latlon', a=semi_major, b=semi_minor)
+ lon, lat, height = pyproj.transform(lla, ecef, record['long_X_East'], record['lat_Y_North'], record['ht'])
+ return lon, lat, height
+
+def apply_transformations(atf_dict, df):
+ """
+ Takes a atf dictionary and a socet dataframe and applies the necessary
+ transformations to convert that dataframe into a isis compatible
+ dataframe
+
+ Parameters
+ ----------
+ atf_dict : dict
+ Dictionary containing information from an atf file
+
+ df : object
+ Pandas dataframe object
+
+ """
+ prj_file = os.path.join(atf_dict['PATH'], atf_dict['PROJECT'].split('\\')[-1])
+
+ eRadius, pRadius = get_axis(prj_file)
+
+ df['s.'], df['l.'], df['image_index'] = (zip(*df.apply(line_sample_size, path = atf_dict['PATH'], axis=1)))
+ df['known'] = df.apply(known, axis=1)
+ df['lat_Y_North'] = df.apply(lat_ISIS_coord, semi_major = eRadius, semi_minor = pRadius, axis=1)
+ df['long_X_East'] = df.apply(lon_ISIS_coord, semi_major = eRadius, semi_minor = pRadius, axis=1)
+ df['long_X_East'], df['lat_Y_North'], df['ht'] = zip(*df.apply(body_fix, semi_major = eRadius, semi_minor = pRadius, 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