From 09b691dc8b01bb40394213b2542d46a178f556c9 Mon Sep 17 00:00:00 2001
From: jlaura <jlaura@asu.edu>
Date: Thu, 1 Feb 2018 14:46:20 -0700
Subject: [PATCH] Updates to the GPF reader/writer (#21)
* Adds prototype socet gpf read from @thareUSGS
* Adds test to gpf reader
* Adds length assertion and logic for dynamic cols
* removed static struct arr
* Finishing the merge cleanly
* removed assertTrue
* Fixes test to compare in/out files.
---
plio/examples/SocetGXP/out_InSightE08_XW.gpf | 803 ------------------
.../Untitled-checkpoint.ipynb | 6 -
plio/io/io_gpf.py | 14 +-
plio/io/tests/test_gpf.py | 34 -
plio/io/tests/test_io_gpf.py | 45 +
5 files changed, 52 insertions(+), 850 deletions(-)
delete mode 100644 plio/examples/SocetGXP/out_InSightE08_XW.gpf
delete mode 100644 plio/io/.ipynb_checkpoints/Untitled-checkpoint.ipynb
delete mode 100644 plio/io/tests/test_gpf.py
create mode 100644 plio/io/tests/test_io_gpf.py
diff --git a/plio/examples/SocetGXP/out_InSightE08_XW.gpf b/plio/examples/SocetGXP/out_InSightE08_XW.gpf
deleted file mode 100644
index 2e9cc29..0000000
--- a/plio/examples/SocetGXP/out_InSightE08_XW.gpf
+++ /dev/null
@@ -1,803 +0,0 @@
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diff --git a/plio/io/.ipynb_checkpoints/Untitled-checkpoint.ipynb b/plio/io/.ipynb_checkpoints/Untitled-checkpoint.ipynb
deleted file mode 100644
index 2fd6442..0000000
--- a/plio/io/.ipynb_checkpoints/Untitled-checkpoint.ipynb
+++ /dev/null
@@ -1,6 +0,0 @@
-{
- "cells": [],
- "metadata": {},
- "nbformat": 4,
- "nbformat_minor": 2
-}
diff --git a/plio/io/io_gpf.py b/plio/io/io_gpf.py
index b5647b0..4d34930 100644
--- a/plio/io/io_gpf.py
+++ b/plio/io/io_gpf.py
@@ -1,4 +1,4 @@
-import numpy as np
+import numpy as np
import pandas as pd
def read_gpf(input_data):
@@ -43,7 +43,7 @@ def read_gpf(input_data):
assert int(cnt) == len(df)
return df
-
+
def save_gpf(df, output_file):
"""
Write a socet gpf file from a gpf-defined pandas dataframe
@@ -55,7 +55,7 @@ def save_gpf(df, output_file):
output_file : str
path to the output data file
-
+
Returns
-------
int : success value
@@ -68,10 +68,10 @@ def save_gpf(df, output_file):
except:
print ('Unable to open output gpf file: {0}'.format(output_file))
return 1
-
+
#grab number of rows in pandas dataframe
numpts = len(df)
-
+
#Output gpf header
outGPF.write('GROUND POINT FILE\n')
outGPF.write('{0}\n'.format(numpts))
@@ -83,6 +83,6 @@ def save_gpf(df, output_file):
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\n'.format(row['res0'], row['res1'], row['res2']))
-
+
outGPF.close()
- return 0
+ return
diff --git a/plio/io/tests/test_gpf.py b/plio/io/tests/test_gpf.py
deleted file mode 100644
index f780d78..0000000
--- a/plio/io/tests/test_gpf.py
+++ /dev/null
@@ -1,34 +0,0 @@
-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.io.io_gpf import save_gpf
-from plio.examples import get_path
-
-import filecmp
-import pytest
-
-@pytest.fixture
-
-def insight_gpf():
- return get_path('InSightE08_XW.gpf')
-
-def out_insight_gpf():
- return get_path('out_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)
-
-@pytest.mark.parametrize('gpf, out_gpf', [(insight_gpf(),out_insight_gpf())])
-def test_write_gfp(gpf, out_gpf):
- df = read_gpf(gpf)
- val = save_gpf(df, out_gpf)
- assertTrue(filecmp.cmp(gpf, out_gpf, shallow=True), "save_gpf does not create an equal file.")
-
diff --git a/plio/io/tests/test_io_gpf.py b/plio/io/tests/test_io_gpf.py
new file mode 100644
index 0000000..d9752c9
--- /dev/null
+++ b/plio/io/tests/test_io_gpf.py
@@ -0,0 +1,45 @@
+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.io.io_gpf import save_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)
+
+@pytest.mark.parametrize('gpf', [(insight_gpf())])
+def test_write_gpf(gpf):
+ """
+ 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')
+
+ with open(gpf) as f:
+ fl = f.readlines()
+
+ with open('out.gpf') as f:
+ fs = f.readlines()
+
+ # Check that the header is the same
+ for i in range(3):
+ assert fl[i] == fs[i]
+
+ truth_arr = np.genfromtxt(gpf, skip_header=3)
+ test_arr = np.genfromtxt('out.gpf', skip_header=3)
+ np.testing.assert_array_almost_equal(truth_arr, test_arr)
--
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