From aaa52d9d51fabcc106e222f63b3bf3a8bb67ed83 Mon Sep 17 00:00:00 2001
From: "David P. Mayer" <dpmayer@usgs.gov>
Date: Mon, 14 Jun 2021 21:02:12 -0700
Subject: [PATCH] Added GXP support to read_gpf() (#164)
* Added GXP support to read_gpf()
Modified read_gpf() in io_bae.py to support reading of either legacy Socet Set-style GPF files or new Socet GXP-style GPF files. Function now takes a boolean, `gxp` to flag whether function should interpret input file as SSET or GXP style, defaulst to SSET style for backwards compatibility. Removed unused variables from read_gpf(). Field names are now hard-coded in the function, rather than generated dynamically. The hints about field names in the GXP-style GPFs are just complicated enough that hard-coding a list of field names into the function was the simplest solution. Datatypes for each field were already hard-coded, so hard-coding the names is stylistically consistent.
Partially address #24
* Deleted extraneous comment
* Added tests for read_gpf() and updated Socet GXP test data
* Updating test for read_gpf(), ticking minor version number
* Fixing fixtures...maybe
* Fixing fixtures...maybe
* Correct variable assignment in read_gpf(), more fixing fixtures
* Fixing test parameterization
* More test parameterization tweaks
---
plio/examples/SocetGXP/GXP_example_gpf.csv | 25 ++
plio/examples/SocetGXP/GXP_example_gpf.gpf | 174 +++++---
.../SocetGXP/GXP_example_wEigenValues.gpf | 391 ------------------
plio/io/io_bae.py | 83 ++--
plio/io/tests/test_io_bae.py | 63 ++-
setup.py | 2 +-
6 files changed, 250 insertions(+), 488 deletions(-)
create mode 100644 plio/examples/SocetGXP/GXP_example_gpf.csv
delete mode 100644 plio/examples/SocetGXP/GXP_example_wEigenValues.gpf
diff --git a/plio/examples/SocetGXP/GXP_example_gpf.csv b/plio/examples/SocetGXP/GXP_example_gpf.csv
new file mode 100644
index 0000000..18d1af7
--- /dev/null
+++ b/plio/examples/SocetGXP/GXP_example_gpf.csv
@@ -0,0 +1,25 @@
+point_id,use,point_type,lat_Y_North,long_X_East,ht,sig0,sig1,sig2,res0,res1,res2,eigenval0,eigenvec0_i,eigenvec0_j,eigenvec0_k,eigenval1,eigenvec1_i,eigenvec1_j,eigenvec1_k,eigenval2,eigenvec2_i,eigenvec2_j,eigenvec2_k
+ESP_011969_1425_REDmos_hijitreged_1,1,0,-37.52498315102231,-168.0378101351008,2166.8567751754185,0.0,0.0,0.0,0.0,0.0,0.0,0.010015,0.991258,-0.131935,-0.000733,0.017375,0.126817,0.951241,0.281173,103723.422751,0.036399,0.278808,-0.959657
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diff --git a/plio/examples/SocetGXP/GXP_example_gpf.gpf b/plio/examples/SocetGXP/GXP_example_gpf.gpf
index c3e1801..196281d 100644
--- a/plio/examples/SocetGXP/GXP_example_gpf.gpf
+++ b/plio/examples/SocetGXP/GXP_example_gpf.gpf
@@ -18,115 +18,197 @@ GXP_Z_UNITS 3
GXP_Z_PRECISION 3
GXP_COORD_FORMAT 3
GXP_COORD_FORMAT_PRECISIONS 4
-22
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-ESP_020297_2045_REDmos_hijitreged_8bit_1 0 0
-24.71012840659569 -18.80031897144174 29.99985045008361
+24
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diff --git a/plio/examples/SocetGXP/GXP_example_wEigenValues.gpf b/plio/examples/SocetGXP/GXP_example_wEigenValues.gpf
deleted file mode 100644
index 7a0607e..0000000
--- a/plio/examples/SocetGXP/GXP_example_wEigenValues.gpf
+++ /dev/null
@@ -1,391 +0,0 @@
-GROUND POINT FILE
-COORD_SYSTEM 1
-ELLIPSOID WGS_84
-REFERENCE_DATUM_CODE WGS_84
-A_EARTH 6.37813700000000e+06
-E_EARTH 8.18191908426520e-02
-ELLIPSOID_CENTER 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
-DATUM_ROTATION 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
-DATUM_SCALE 1.00000000000000e+00
-DATUM_USE_APPROXIMATE 0
-VERTICAL_REFERENCE 0
-GEOID EGM96
-GXP_GEO_DELIM 0
-XY_UNITS 2
-Z_UNITS 1
-GXP_XY_UNITS 8
-GXP_Z_UNITS 3
-GXP_Z_PRECISION 3
-GXP_COORD_FORMAT 3
-GXP_COORD_FORMAT_PRECISIONS 4
-48
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diff --git a/plio/io/io_bae.py b/plio/io/io_bae.py
index 55d1832..b269bc8 100644
--- a/plio/io/io_bae.py
+++ b/plio/io/io_bae.py
@@ -3,7 +3,7 @@ import os
import json
from collections import defaultdict
from functools import singledispatch
-
+from linecache import getline
import numpy as np
import pandas as pd
@@ -193,61 +193,70 @@ def save_ipf(df, output_path):
outIPF.close()
return
-def read_gpf(input_data):
+def read_gpf(input_data,gxp=False):
"""
Read a socet gpf file into a pandas data frame
Parameters
----------
- input_file : str
+ input_data : str
path to the input data file
+ gxp : bool
+ Flag to notify function if input_data follows Socet GXP format.
+ Defaults is False (assume Socet Set format).
+
Returns
-------
df : pd.DataFrame
containing the gpf 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
-
- 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])
+ # line containing point count differs between Socet Set and Socet GXP gpf files
+ if not gxp:
+ l = 2
+ else:
+ l = 21
- for column_num in range(int(num)):
- new_column = '{}{}'.format(column_name, column_num)
- columns.append(new_column);
+ cnt = getline(input_data, l)
+ cnt = int(cnt)
+
+ # Lists of column names and their data types
+ if not gxp:
+ columns = ['point_id','stat','known','lat_Y_North','long_X_East','ht','sig0','sig1','sig2','res0','res1','res2']
+ col_dtype = ['str','int32','int32','float64','float64','float64','float64','float64','float64','float64','float64','float64']
+ else:
+ columns = ['point_id','use','point_type','lat_Y_North','long_X_East','ht','sig0','sig1','sig2','res0','res1','res2',
+ 'eigenval0','eigenvec0_i','eigenvec0_j', 'eigenvec0_k',
+ 'eigenval1','eigenvec1_i','eigenvec1_j', 'eigenvec1_k',
+ 'eigenval2','eigenvec2_i','eigenvec2_j', 'eigenvec2_k']
+ col_dtype = ['str','int32','int32','float64','float64','float64','float64','float64','float64','float64','float64','float64',
+ 'float64','float64','float64','float64',
+ 'float64','float64','float64','float64',
+ 'float64','float64','float64','float64']
- else:
- columns.append(column)
+ # Build dict of column names and their data types
+ dtype_dict = dict(zip(columns, col_dtype))
- # 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)
+ if not gxp:
+ # Mixed types requires read as unicode - let pandas soft convert
+ d = np.genfromtxt(input_data, skip_header=(l+1), dtype='unicode')
+ d = d.reshape(-1, len(columns))
+ else:
+ # Read GXP-style GPF a block at a time
+ lmax=( (l+1) + ((cnt-1)*8) + 2 )
+ for x in range(l+1,lmax,8):
+ a = np.genfromtxt(input_data, skip_header=(x), max_rows=4, dtype='unicode')
+ b = np.genfromtxt(input_data, skip_header=(x+4), max_rows=3, dtype='unicode')
+ if x == (l+1):
+ d = np.hstack([np.hstack(a),np.hstack(b)])
+ else:
+ d = np.vstack(( d, np.hstack([np.hstack(a),np.hstack(b)])) )
df = pd.DataFrame(d, columns=columns)
- # List of data types for columns in Socet set GPF file
- col_dtype = ['str','int32','int32','float64','float64','float64','float64','float64','float64','float64','float64','float64']
-
- # Build dict of column names and their data types
- dtype_dict = dict(zip(columns, col_dtype))
-
- # Hard conversion of data types to ensure 'point_id' is treated as string and 'stat' and 'known' flags treated as int
+ # Hard conversion of data types to ensure 'point_id' is treated as string and 'stat' and 'known' (GXP: 'use', 'point_type')
+ # flags treated as int
df = df.astype(dtype_dict)
# Validate the read data with the header point count
diff --git a/plio/io/tests/test_io_bae.py b/plio/io/tests/test_io_bae.py
index e3cc729..4031703 100644
--- a/plio/io/tests/test_io_bae.py
+++ b/plio/io/tests/test_io_bae.py
@@ -1,4 +1,4 @@
-'''import json
+import json
import os
import numpy as np
@@ -14,11 +14,15 @@ import pytest
def insight_gpf():
return get_path('InSightE08_XW.gpf')
+@pytest.fixture
+def gxp_gpf():
+ return get_path('GXP_example_gpf.gpf')
+
@pytest.fixture
def example_str_id_gpf():
return get_path('InSightE08_string_id.gpf')
-@pytest.fixture()
+@pytest.fixture
def insight_expected_gpf():
dtype_dict = {'point_id': 'str',
'stat': 'int32',
@@ -35,6 +39,34 @@ def insight_expected_gpf():
return pd.read_csv(get_path('InSightE08_XW.csv'), dtype=dtype_dict)
@pytest.fixture
+def gxp_expected_gpf():
+ dtype_dict = {'point_id': 'str',
+ 'use': 'int32',
+ 'point_type': 'int32',
+ 'lat_Y_North': 'float64',
+ 'long_X_East': 'float64',
+ 'ht': 'float64',
+ 'sig0': 'float64',
+ 'sig1': 'float64',
+ 'sig2': 'float64',
+ 'res0': 'float64',
+ 'res1': 'float64',
+ 'res2': 'float64',
+ 'eigenval0': 'float64',
+ 'eigenvec0_i': 'float64',
+ 'eigenvec0_j': 'float64',
+ 'eigenvec0_k': 'float64',
+ 'eigenval1': 'float64',
+ 'eigenvec1_i': 'float64',
+ 'eigenvec1_j': 'float64',
+ 'eigenvec1_k': 'float64',
+ 'eigenval2': 'float64',
+ 'eigenvec2_i': 'float64',
+ 'eigenvec2_j': 'float64',
+ 'eigenvec2_k': 'float64'}
+ return pd.read_csv(get_path('GXP_example_gpf.csv'), dtype=dtype_dict)
+
+'''@pytest.fixture
def insight_ipf():
return get_path('P20_008845_1894_XN_09N203W.ipf')
@@ -62,13 +94,18 @@ def insight_expected_ipf():
def test_read_ipf(ipf, expected):
df = read_ipf(ipf)
assert_frame_equal(df, expected)
-
-@pytest.mark.parametrize('gpf, expected', [(insight_gpf(),insight_expected_gpf())])
-def test_read_gpf(gpf, expected):
- df = read_gpf(gpf)
- assert_frame_equal(df, expected)
-
-@pytest.mark.parametrize('ipf, file', [(insight_ipf(), 'plio/io/tests/temp')])
+'''
+# @pytest.mark.parametrize('gpf, expected', [ (get_path('InSightE08_XW.gpf'),insight_expected_gpf() ) ] )
+def test_read_gpf(insight_gpf, insight_expected_gpf):
+ df = read_gpf(insight_gpf)
+ assert_frame_equal(df, insight_expected_gpf)
+
+# @pytest.mark.parametrize('gpf, expected', [ (get_path('GXP_example_gpf.gpf'),gxp_expected_gpf() ) ] )
+def test_read_gxp_gpf(gxp_gpf, gxp_expected_gpf):
+ df = read_gpf(gxp_gpf,gxp=True)
+ assert_frame_equal(df, gxp_expected_gpf)
+
+'''@pytest.mark.parametrize('ipf, file', [(insight_ipf(), 'plio/io/tests/temp')])
def test_write_ipf(ipf, file):
df = read_ipf(ipf)
save_ipf(df, file)
@@ -163,8 +200,8 @@ def test_write_str_id_gpf(gpf, file):
# Test that every 5th line (the lines containing the point ID and integer flags) matches
for i in range(3,len(fs),5):
assert fs[i] == fl[i]
-
-@pytest.mark.parametrize('gpf', [(example_str_id_gpf())])
+'''
+@pytest.mark.parametrize('gpf', [get_path('InSightE08_string_id.gpf')])
def test_gpf_dtypes(gpf):
"""
This test makes sure that a GPF whose point IDs only contain numbers
@@ -182,7 +219,7 @@ def test_gpf_dtypes(gpf):
# Check that the type of each column matches the truth list
assert truth_dtypes == test_dtypes
-@pytest.mark.parametrize('ipf', [(example_str_id_ipf())])
+'''@pytest.mark.parametrize('ipf', [(example_str_id_ipf())])
def test_ipf_dtypes(ipf):
"""
This test makes sure that a IPF whose point IDs only contain numbers
@@ -244,4 +281,4 @@ B 1.0e-01 2.000000e+00 3.00000000000000e+00"""
assert len(data['B']) == 3
assert data['B'] == [0.1, 2, 3]
-'''
\ No newline at end of file
+'''
diff --git a/setup.py b/setup.py
index c0ba904..b1ead3c 100644
--- a/setup.py
+++ b/setup.py
@@ -8,7 +8,7 @@ with open('README.md', 'r') as f:
def setup_package():
setup(
name = "plio",
- version = '1.3.0',
+ version = '1.4.0',
author = "USGS Astrogeology",
author_email = "jlaura@usgs.gov",
description = ("I/O API to support planetary data formats."),
--
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