Merge pull request #35 from acpaquette/ipf (d28ee394) · Commits · aflab / astrogeology / Plio

notebooks/Socet2ISIS.ipynb

+1959 −82

File changed.

Preview size limit exceeded, changes collapsed.

plio/examples/SocetGXP/InSightE08_XW.csv

+1 −1

Original line number	Diff line number	Diff line
		point_id,stat,known,lat_Y_North,long_X_East,ht,sigma0,sigma1,sigma2,res0,res1,res2
		point_id,stat,known,lat_Y_North,long_X_East,ht,sig0,sig1,sig2,res0,res1,res2
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		2,1,1,0.08508542650082002,2.3808135855714703,-2702.0,0.0,0.0,1.0,15.983285999999998,-16.869508,0.103341
		3,1,1,0.08626480095809,2.3870838392611,-2714.16003756809,0.0,0.0,3.828854,12.831839,-34.360639,-2.2058459999999998

plio/examples/SocetSet/P20_008845_1894_XN_09N203W.csv

0 → 100644

+122 −0

Original line number	Diff line number	Diff line
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		P03_002226_1895_XI_09N203W_74,1,0,1,-1463.276489,270.004364,0.141123,0.141123,0.097608,0.000572,0.0,0.0
		P03_002226_1895_XI_09N203W_76,1,0,1,-1399.385376,210.815338,0.141123,0.141123,-0.021339,-0.000335,0.0,0.0
		P03_002226_1895_XI_09N203W_82,1,0,1,-1110.612061,-112.804382,0.141123,0.141123,-0.179249,0.431591,0.0,0.0
		P19_008344_1894_XN_09N203W_2,1,0,1,-3987.0656740000004,-1756.185791,0.141123,0.141123,0.018394,-0.141215,0.0,0.0
		P19_008344_1894_XN_09N203W_7,1,0,1,-3991.17334,1967.117554,0.141123,0.141123,0.242488,-0.04689,0.0,0.0
		P03_002371_1888_XI_08N204W_76,1,0,1,4066.5737299999996,1038.447998,0.141123,0.141123,-0.272976,0.9673510000000001,0.0,0.0
		P03_002371_1888_XI_08N204W_78,1,0,1,4083.8732909999994,1277.689209,0.141123,0.141123,-0.328486,0.8362860000000001,0.0,0.0
		P01_001606_1897_XI_09N203W_19,1,0,1,-3917.203125,-1175.195679,0.141123,0.141123,-0.022262999999999998,-0.15115599999999998,0.0,0.0
		P01_001606_1897_XI_09N203W_65,1,0,1,4070.48584,-2315.9921879999997,0.141123,0.141123,-0.12137,-0.47907,0.0,0.0
		P03_002226_1895_XI_09N203W_1,1,0,0,-1197.647949,-569.925598,0.0,0.0,-0.070627,0.194853,0.0,0.0
		P03_002226_1895_XI_09N203W_2,1,0,0,-1241.685791,-499.006836,0.0,0.0,-0.066482,0.270447,0.0,0.0

plio/io/io_bae.py

+97 −12

Original line number	Diff line number	Diff line
		import json
		import re
		from functools import singledispatch

		import numpy as np
		import pandas as pd
		@@ -52,6 +53,77 @@ def socetset_keywords_to_json(keywords, ell=None):
		parse(ell)
		return json.dumps(stream)

		@singledispatch
		def read_ipf(arg): # pragma: no cover
		return str(arg)

		@read_ipf.register(str)
		def read_ipf_str(input_data):
		"""
		Read a socet ipf file into a pandas data frame

		Parameters
		----------
		input_data : str
		path to the an input data file

		Returns
		-------
		df : pd.DataFrame
		containing the ipf data with appropriate column names and indices
		"""

		# Check that the number of rows is matching the expected number
		with open(input_data, 'r') as f:
		for i, l in enumerate(f):
		if i == 1:
		cnt = int(l)
		elif i == 2:
		col = l
		break

		columns = np.genfromtxt(input_data, skip_header=2, dtype='unicode',
		max_rows = 1, delimiter = ',')

		# TODO: Add unicode conversion
		d = [line.split() for line in open(input_data, 'r')]
		d = np.hstack(np.array(d[3:]))

		d = d.reshape(-1, 12)

		df = pd.DataFrame(d, columns=columns)

		assert int(cnt) == len(df), 'Dataframe length {} does not match point length {}.'.format(int(cnt), len(df))

		# Soft conversion of numeric types to numerics, allows str in first col for point_id
		df = df.apply(pd.to_numeric, errors='ignore')

		return df

		@read_ipf.register(list)
		def read_ipf_list(input_data_list):
		"""
		Read a socet ipf file into a pandas data frame

		Parameters
		----------
		input_data_list : list
		list of paths to the a set of input data files

		Returns
		-------
		df : pd.DataFrame
		containing the ipf data with appropriate column names and indices
		"""
		frames = []

		for input_file in input_data_list:
		frames.append(read_ipf(input_file))

		df = pd.concat(frames)

		return df

		def read_gpf(input_data):
		"""
		Read a socet gpf file into a pandas data frame
		@@ -76,22 +148,35 @@ def read_gpf(input_data):
		col = l
		break

		default_columns = np.genfromtxt(input_data, skip_header=2, dtype='unicode',
		max_rows = 1, delimiter = ',')

		columns = []

		for column in default_columns:

		if '(' in column and ')' in column:
		column_name ,suffix = column.split('(')
		num = int(suffix.split(')')[0])

		for column_num in range(int(num)):
		new_column = '{}{}'.format(column_name, column_num)
		columns.append(new_column);

		else:
		columns.append(column)

		# Mixed types requires read as unicode - let pandas soft convert
		d = np.genfromtxt(input_data, skip_header=3, dtype='unicode')
		d = d.reshape(-1, 12)

		#TODO: cols should be used to dynamically generate the column names

		df = pd.DataFrame(d, columns=['point_id', 'stat', 'known',
		'lat_Y_North', 'long_X_East','ht',
		'sigma0', 'sigma1', 'sigma2',
		'res0', 'res1', 'res2'])
		df = pd.DataFrame(d, columns=columns)

		# Soft conversion of numeric types to numerics, allows str in first col for point_id
		df = df.apply(pd.to_numeric, errors='ignore')

		# Validate the read data with the header point count
		assert int(cnt) == len(df)
		assert int(cnt) == len(df), 'Dataframe length {} does not match point length {}.'.format(int(cnt), len(df))

		return df

		@@ -132,7 +217,7 @@ def save_gpf(df, output_file):
		#Output coordinates to gpf file
		outGPF.write('{0} {1} {2}\n'.format(row['point_id'], row['stat'], row['known']))
		outGPF.write('{0} {1} {2}\n'.format(row['lat_Y_North'], row['long_X_East'], row['ht']))
		outGPF.write('{0} {1} {2}\n'.format(row['sigma0'], row['sigma1'], row['sigma2']))
		outGPF.write('{0} {1} {2}\n'.format(row['sig0'], row['sig1'], row['sig2']))
		outGPF.write('{0} {1} {2}\n\n'.format(row['res0'], row['res1'], row['res2']))

		outGPF.close()

plio/io/tests/test_io_bae.py

+24 −10

Original line number	Diff line number	Diff line
		import json

		import numpy as np
		import pandas as pd
		from pandas.util.testing import assert_frame_equal

		from plio.io.io_bae import socetset_keywords_to_json, read_gpf, save_gpf
		from plio.io.io_bae import socetset_keywords_to_json, read_gpf, save_gpf, read_ipf
		from plio.examples import get_path

		import pytest
		@@ -13,27 +14,40 @@ def insight_gpf():
		return get_path('InSightE08_XW.gpf')

		@pytest.fixture()
		def insight_expected():
		def insight_expected_gpf():
		return pd.read_csv(get_path('InSightE08_XW.csv'))

		@pytest.mark.parametrize('gpf, expected', [(insight_gpf(),insight_expected())])
		@pytest.fixture
		def insight_ipf():
		return get_path('P20_008845_1894_XN_09N203W.ipf')

		@pytest.fixture()
		def insight_expected_ipf():
		return pd.read_csv(get_path('P20_008845_1894_XN_09N203W.csv'))

		@pytest.mark.parametrize('gpf, expected', [(insight_gpf(),insight_expected_gpf())])
		def test_read_gfp(gpf, expected):
		df = read_gpf(gpf)
		assert_frame_equal(df, expected)

		@pytest.mark.parametrize('gpf', [(insight_gpf())])
		def test_write_gpf(gpf):
		@pytest.mark.parametrize('ipf, expected', [([insight_ipf()],insight_expected_ipf())])
		def test_read_ifp(ipf, expected):
		df = read_ipf(ipf)
		assert_frame_equal(df, expected)

		@pytest.mark.parametrize('gpf, file', [(insight_gpf(), 'out.gpf')])
		def test_write_gpf(gpf, file):
		"""
		We test by manually comparing files and not using filecmp so that we
		are not testing float point precision differences, e.g. 0.0 == 0.00000000.
		"""
		df = read_gpf(gpf)
		save_gpf(df, 'out.gpf')
		save_gpf(df, file)

		with open(gpf) as f:
		fl = f.readlines()

		with open('out.gpf') as f:
		with open(file) as f:
		fs = f.readlines()

		# Check that the header is the same
		@@ -41,7 +55,7 @@ def test_write_gpf(gpf):
		assert fl[i] == fs[i]

		truth_arr = np.genfromtxt(gpf, skip_header=3)
		test_arr = np.genfromtxt('out.gpf', skip_header=3)
		test_arr = np.genfromtxt(file, skip_header=3)
		np.testing.assert_array_almost_equal(truth_arr, test_arr)

		def test_create_from_socet_lis():