From ed5e2ce5a650341528b5053f31303b03ec6fcaee Mon Sep 17 00:00:00 2001
From: jlaura <jlaura@asu.edu>
Date: Wed, 31 Jan 2018 12:25:40 -0700
Subject: [PATCH] Adds Socet GPF reads into plio (#18)
* Adds prototype socet gpf read from @thareUSGS
* Adds test to gpf reader
* Adds length assertion and logic for dynamic cols
* removed static struct arr
---
plio/examples/SocetGXP/InSightE08_XW.csv | 161 +++++
plio/examples/SocetGXP/InSightE08_XW.gpf | 803 +++++++++++++++++++++++
plio/io/io_gpf.py | 46 ++
plio/io/tests/test_gpf.py | 21 +
4 files changed, 1031 insertions(+)
create mode 100644 plio/examples/SocetGXP/InSightE08_XW.csv
create mode 100644 plio/examples/SocetGXP/InSightE08_XW.gpf
create mode 100644 plio/io/io_gpf.py
create mode 100644 plio/io/tests/test_gpf.py
diff --git a/plio/examples/SocetGXP/InSightE08_XW.csv b/plio/examples/SocetGXP/InSightE08_XW.csv
new file mode 100644
index 0000000..29e9480
--- /dev/null
+++ b/plio/examples/SocetGXP/InSightE08_XW.csv
@@ -0,0 +1,161 @@
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diff --git a/plio/examples/SocetGXP/InSightE08_XW.gpf b/plio/examples/SocetGXP/InSightE08_XW.gpf
new file mode 100644
index 0000000..b901ab8
--- /dev/null
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diff --git a/plio/io/io_gpf.py b/plio/io/io_gpf.py
new file mode 100644
index 0000000..5b46938
--- /dev/null
+++ b/plio/io/io_gpf.py
@@ -0,0 +1,46 @@
+import math
+import numpy as np
+import pandas as pd
+
+def read_gpf(input_data):
+ """
+ Read a socet gpf file into a pandas data frame
+
+ Parameters
+ ----------
+ input_file : str
+ path to the input data file
+
+ Returns
+ -------
+ df : pd.DataFrame
+ containing the gfp 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
+
+ # 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'])
+
+ # 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)
+
+ return df
diff --git a/plio/io/tests/test_gpf.py b/plio/io/tests/test_gpf.py
new file mode 100644
index 0000000..95379e2
--- /dev/null
+++ b/plio/io/tests/test_gpf.py
@@ -0,0 +1,21 @@
+import numpy as np
+import pandas as pd
+from pandas.util.testing import assert_frame_equal
+
+from plio.io.io_gpf import read_gpf
+from plio.examples import get_path
+
+import pytest
+
+@pytest.fixture
+def insight_gpf():
+ return get_path('InSightE08_XW.gpf')
+
+@pytest.fixture()
+def insight_expected():
+ return pd.read_csv(get_path('InSightE08_XW.csv'))
+
+@pytest.mark.parametrize('gpf, expected', [(insight_gpf(),insight_expected())])
+def test_read_gfp(gpf, expected):
+ df = read_gpf(gpf)
+ assert_frame_equal(df, expected)
--
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