diff --git a/.travis.yml b/.travis.yml
index 2d2e09d128b335233fa9baaf909e17292fe3f9d1..d05d2d04c1dfbb63fcf1d23242f483701dea28ba 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -37,7 +37,7 @@ install:
- conda config --add channels conda-forge
- conda install -q gdal h5py pandas sqlalchemy pyyaml networkx affine protobuf scipy pvl
# Development installation
- - conda install -q pytest pytest-cov sh
+ - conda install -q pytest pytest-cov sh coveralls nbsphinx
script:
- pytest --cov=plio
@@ -51,7 +51,8 @@ after_success:
- conda build --token $CONDA_UPLOAD_TOKEN --python $PYTHON_VERSION recipe -q
# Docs to gh-pages
- - source activate test_env # Reactivate the env to have all deps installed.
+ - source activate test # Reactivate the env to have all deps installed.
+ - pip install travis-sphinx
- travis-sphinx build --source=docs --nowarn # The sphinx build script
- travis-sphinx deploy --branches=dev
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
new file mode 100644
index 0000000000000000000000000000000000000000..2fe05808f4f518ef9f7586cf31bd3cfb57c5cb22
--- /dev/null
+++ b/bin/socet2isis
@@ -0,0 +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):
+ # 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())
diff --git a/plio/data/data.db b/plio/data/data.db
index c1ac0e7c5802a4222a93a6ab400dc3dbc454aeb0..09fc46d99adf6d88099df74c72033a853cc3e8eb 100644
Binary files a/plio/data/data.db and b/plio/data/data.db differ
diff --git a/plio/examples/CTX/ctx.pvl b/plio/examples/CTX/ctx.pvl
new file mode 100644
index 0000000000000000000000000000000000000000..b062798ad7043009e8c98e607ea39122b6b80c18
--- /dev/null
+++ b/plio/examples/CTX/ctx.pvl
@@ -0,0 +1,72 @@
+Object = IsisCube
+ Object = Core
+ StartByte = 65537
+ Format = Tile
+ TileSamples = 1000
+ TileLines = 1024
+
+ Group = Dimensions
+ Samples = 5000
+ Lines = 7168
+ Bands = 1
+ End_Group
+
+ Group = Pixels
+ Type = SignedWord
+ ByteOrder = Lsb
+ Base = 0.0
+ Multiplier = 1.0
+ End_Group
+ End_Object
+
+ Group = Instrument
+ SpacecraftName = Mars_Reconnaissance_Orbiter
+ InstrumentId = CTX
+ TargetName = Mars
+ MissionPhaseName = PSP
+ StartTime = 2008-09-17T05:08:10.820
+ SpacecraftClockCount = 0906095311:038
+ OffsetModeId = 196/190/181
+ LineExposureDuration = 1.877 <MSEC>
+ FocalPlaneTemperature = 293.4 <K>
+ SampleBitModeId = SQROOT
+ SpatialSumming = 1
+ SampleFirstPixel = 0
+ End_Group
+
+ Group = Archive
+ DataSetId = MRO-M-CTX-2-EDR-L0-V1.0
+ ProductId = B01_010045_1878_XN_07N205W
+ ProducerId = MRO_CTX_TEAM
+ ProductCreationTime = 2009-04-13T19:24:46
+ OrbitNumber = 10045
+ End_Group
+
+ Group = BandBin
+ FilterName = BroadBand
+ Center = 0.65 <micrometers>
+ Width = 0.15 <micrometers>
+ End_Group
+
+ Group = Kernels
+ NaifFrameCode = -74021
+ LeapSecond = $base/kernels/lsk/naif0012.tls
+ TargetAttitudeShape = $base/kernels/pck/pck00009.tpc
+ TargetPosition = (Table, $base/kernels/spk/de405.bsp)
+ InstrumentPointing = (Table,
+ $mro/kernels/ck/mro_sc_psp_080916_080922.bc,
+ $mro/kernels/fk/mro_v15.tf)
+ Instrument = Null
+ SpacecraftClock = $mro/kernels/sclk/MRO_SCLKSCET.00064.65536.tsc
+ InstrumentPosition = (Table, $mro/kernels/spk/mro_psp8.bsp)
+ InstrumentAddendum = $mro/kernels/iak/mroctxAddendum005.ti
+ ShapeModel = $base/dems/molaMarsPlanetaryRadius0005.cub
+ InstrumentPositionQuality = Reconstructed
+ InstrumentPointingQuality = Reconstructed
+ CameraVersion = 1
+ End_Group
+End_Object
+
+Object = Label
+ Bytes = 65536
+End_Object
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/io/io_db.py b/plio/io/io_db.py
index a8a7e259194f46603ace04368d9065e1c2c43503..988ec589fed803328d139a578fff260b7fc972d1 100644
--- a/plio/io/io_db.py
+++ b/plio/io/io_db.py
@@ -41,6 +41,10 @@ class Translations(Base): # pragma: no cover
self.instrument = instrument
self.translation = translation
+ def __repr__(self):
+ return 'Mission: {}\nInstrument: {}\nTranslation: {}'.format(self.mission,
+ self.instrument,
+ self.translation)
class StringToMission(Base): # pragma: no cover
"""
diff --git a/plio/io/isis_serial_number.py b/plio/io/isis_serial_number.py
index 0c187abff1a0ea0fbe70fe3781dca7fc092f035f..01f8fb7d3d0b5256fea5c7c99a21e4de31fecbe6 100644
--- a/plio/io/isis_serial_number.py
+++ b/plio/io/isis_serial_number.py
@@ -82,6 +82,7 @@ def generate_serial_number(label):
# Sort the keys to ensure proper iteration order
keys = sorted(translation.keys())
+
for k in keys:
try:
group = translation[k]
diff --git a/plio/io/tests/test_isis_serial_numbers.py b/plio/io/tests/test_isis_serial_numbers.py
index 8abf3227fa9f5c98904fbf3348911c58f3d0eeb2..2cd68907e17432dc2a72f9a315102a51e025b76d 100644
--- a/plio/io/tests/test_isis_serial_numbers.py
+++ b/plio/io/tests/test_isis_serial_numbers.py
@@ -1,17 +1,24 @@
import os
import sys
-import unittest
-from plio.examples import get_path
-
-sys.path.insert(0, os.path.abspath('..'))
+import pytest
from plio.io import isis_serial_number
+from plio.examples import get_path
+
+@pytest.fixture
+def apollo_lbl():
+ return get_path('Test_PVL.lbl')
+@pytest.fixture
+def ctx_lbl():
+ return get_path('ctx.pvl')
-class TestIsisSerials(unittest.TestCase):
+@pytest.mark.parametrize("label, expected", [(apollo_lbl(), 'APOLLO15/METRIC/1971-07-31T14:02:27.179'),
+ (ctx_lbl(),'MRO/CTX/0906095311:038')
+ ])
+def test_generate_serial_number(label, expected):
+ serial = isis_serial_number.generate_serial_number(label)
+ assert serial == expected
- def test_generate_serial_number(self):
- label = get_path('Test_PVL.lbl')
- serial = isis_serial_number.generate_serial_number(label)
- self.assertEqual('APOLLO15/METRIC/1971-07-31T14:02:27.179', serial)
\ No newline at end of file
+
\ No newline at end of file
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
diff --git a/setup.py b/setup.py
index 0431bad1067c6fdb5d4a085d2896076ace9cd3d6..6932e2f2e29d75c78259d5c72149c418fd6c87fe 100644
--- a/setup.py
+++ b/setup.py
@@ -36,6 +36,7 @@ def setup_package():
package_data={'plio' : list(examples) + ['data/*.db', 'data/*.py'] +\
['sqlalchemy_json/*.py', 'sqlalchemy_json/LICENSE']},
zip_safe=False,
+ scripts=['bin/socet2isis'],
install_requires=[
'gdal',
'numpy',