def test(target=None, show=False, onlydoctests=False, coverage=False, htmlreport=False):
"""Run docstring examples and additional tests.
Examples
--------
>>> from pygimli.utils import boxprint
>>> test(target=boxprint)
Parameters
----------
target : function, optional
Function or method to test. By default everything is tested.
show : boolean, optional
Show matplotlib windows during test run. They will be closed
automatically.
onlydoctests : boolean, optional
Run test files in ../tests as well.
coverage : boolean, optional
Create a coverage report. Requires the pytest-cov plugin.
htmlreport : str, optional
Filename for HTML report such as www.pygimli.org/build_tests.html.
Requires pytest-html plugin.
"""
if target:
import doctest
doctest.run_docstring_examples(target, globals())
return
try:
import pytest
except ImportError:
raise ImportError("pytest is required to run test suite. " + \
"Try 'sudo pip install pytest'.")
from matplotlib import pyplot as plt
from pygimli.utils import opt_import
pc = opt_import("pytest_cov", "create a code coverage report")
ph = opt_import("pytest_html", "create a html report")
old_backend = plt.get_backend()
if not show:
plt.switch_backend("Agg")
cwd = os.path.realpath(__path__[0])
cfg = os.path.join(cwd, "../tests/setup.cfg")
cmd = ""
if os.path.exists(cfg):
cmd += "-c %s " % cfg
if pc and coverage:
cmd += "--cov pygimli --cov-report term " + \
"--cov-config %s " % cfg.replace("setup.cfg", ".coveragerc")
if ph and htmlreport:
cmd += "--html %s " % htmlreport
cmd += "%s " % cwd
if not onlydoctests and os.path.exists(cfg):
cmd += os.path.join(cwd, "../tests")
exitcode = pytest.main(cmd)
plt.switch_backend(old_backend)
plt.close('all')
sys.exit(exitcode)
def GKtoUTM(R, H=None, zone=32, gk=None, gkzone=None):
"""Transforms any Gauss-Krueger to UTM autodetect GK zone from offset."""
if gk is None and gkzone is None:
if H is None:
rr = R[0][0]
else:
if isinstance(R, list) or isinstance(R, tuple):
rr = R[0]
else:
rr = R
gkzone = int(floor(rr * 1e-6))
print(gkzone)
if gkzone <= 0 or gkzone >= 5:
print("cannot detect valid GK zone")
pyproj = opt_import('pyproj', 'coordinate transformations')
if pyproj is None:
return None
gk = pyproj.Proj(init="epsg:"+str(31464+gkzone))
wgs84 = pyproj.Proj(init="epsg:4326") # pure ellipsoid to doubel transform
utm = pyproj.Proj(proj='utm', zone=zone, ellps='WGS84') # UTM
if H is None: # two-column matrix
lon, lat = pyproj.transform(gk, wgs84, R[0], R[1])
else:
lon, lat = pyproj.transform(gk, wgs84, R, H)
return utm(lon, lat)
def test(show=False, coverage=False):
"""Test all code examples in docstrings using pytest."""
try:
import pytest
except ImportError:
raise ImportError("pytest is required to run test suite. " + "Try 'sudo pip install pytest'.")
from matplotlib import pyplot as plt
from pygimli.utils import opt_import
pc = opt_import("pytest_cov", "create a coverage report")
old_backend = plt.get_backend()
if not show:
plt.switch_backend("Agg")
cwd = __path__[0]
cfg = os.path.join(cwd, "../tests/setup.cfg")
cmd = ""
if os.path.exists(cfg):
cmd += "-c %s " % cfg
if pc and coverage:
cmd += "--cov pygimli --cov-report coveralls --cov-report html " + "--cov-config %s " % cfg.replace(
"setup.cfg", ".coveragerc"
)
cmd += "%s" % cwd
try:
pytest.main(cmd)
finally:
plt.switch_backend(old_backend)
def _load(self, polyfile):
"""
Read polygon info from XML file.
Example of XML file:
"""
ET = opt_import("xml.etree.cElementTree", "read in XML files")
self.doc = ET.parse(polyfile)
self._parse()
# -*- coding: utf-8 -*-
from pygimli.gui.mpl import AppResourceMPL
from pygimli.importexport import readGPX, readSimpleLatLon
from pygimli.mplviewer import underlayMap
from pygimli.utils import opt_import
pyproj = opt_import('pyproj', 'coordinate transformations of EM data')
def findUTMZone(lon, lat):
"""
find utm zone for lon and lat values.
Return str(zone)+hemisphere
lon -180 -- -174 -> 1 ... 174 -- 180 -> 60
lat < 0 hemisphere = S, > 0 hemisphere = N
"""
zone = (int(lon) + 180) / 6 + 1
if lat > 0:
return str(zone) + 'N'
else:
return str(zone) + 'S'
# def findUTMZone(...)
class GPSViewerApp(AppResourceMPL):
"""
def readHEMData(self, filename, takeevery=1, choosevcp=True):
""" read RESOLVE type airborne EM data from .XYZ file """
self.header = {}
keyword = ''
with open(filename) as f:
for i, line in enumerate(f):
if line[0] == '/':
line = line[1:].strip('\n').replace(',', '').replace('AND',
'')
try:
result = [float(co) for co in line.split()]
except:
result = line.split()
if len(result) == 1:
result = result[0]
if keyword:
if isinstance(keyword, list):
for kw, res in zip(keyword, result):
self.header[kw] = res
else:
self.header[keyword] = result
keyword = ''
else:
keyword = result
else:
break
line = f.readline()
print(line)
# tmp = np.genfromtxt(fname=f, autostrip=True, comments='/',
# skip_header=0, dtype=float, names=1, case_sensitive='lower',
# missing_values='*', filling_values=-9999, skip_footer=1)
tmp = np.genfromtxt(
fname=filename, autostrip=True, comments='/',
skip_header=i+1, dtype=float, names=True, case_sensitive='lower',
missing_values='*', filling_values=-9999, skip_footer=1)
# read properties from header
if choosevcp:
ivcp = np.nonzero(np.array(self.header['COILGEOMETRY']) == 1)[0]
else:
ivcp = range(len(self.header['FREQUENCY']))
self.frequencies = np.array(self.header['FREQUENCY'])[ivcp]
self.coilSpacing = np.array(self.header['COILSEPERATION'])[ivcp]
# read properties from data block
names = tmp.dtype.names
pyproj = opt_import('pyproj', 'coordinate transformations EM lon,lat values')
if 'lon' in names and 'lat' in names and pyproj is not None:
utm = pyproj.Proj(proj='utm', zone=32, ellps='WGS84') # projection
x, y = utm(tmp['lon'], tmp['lat'])
else:
x, y = tmp['x'], tmp['y']
self.pos = np.column_stack((x, y))[::takeevery]
dx = np.sqrt(np.diff(self.pos[:, 0])**2 + np.diff(self.pos[:, 1])**2)
self.x = np.hstack((0., np.cumsum(dx)))
self.z = tmp['h_laser'][::takeevery]
self.topo = tmp['topo'][::takeevery]
IP = np.column_stack([tmp['real_'+str(i+1)] for i in ivcp])
OP = np.column_stack([tmp['quad_'+str(i+1)] for i in ivcp])
# better do a decimation or running average here
self.IP = IP[::takeevery, :]
self.OP = OP[::takeevery, :]
self.isActiveFreq = self.frequencies > 0.0
self.activeFreq = np.nonzero(self.isActiveFreq)[0]
# -*- coding: utf-8 -*-
from pygimli.gui.mpl import AppResourceMPL
from pygimli.importexport import readGPX, readSimpleLatLon
from pygimli.mplviewer import underlayMap
from pygimli.utils import opt_import
pyproj = opt_import('pyproj', 'coordinate transformations of EM data')
def findUTMZone(lon, lat):
"""
find utm zone for lon and lat values.
Return str(zone)+hemisphere
lon -180 -- -174 -> 1 ... 174 -- 180 -> 60
lat < 0 hemisphere = S, > 0 hemisphere = N
"""
zone = (int(lon) + 180) / 6 + 1
if lat > 0:
return str(zone) + 'N'
else:
return str(zone) + 'S'
# def findUTMZone(...)
class GPSViewerApp(AppResourceMPL):
"""
from pygimli.utils import opt_import
json = opt_import("json", "read and write inversion settings")
class InversionSettings(dict):
"""
Extends the built-in dict with methods for saving and loading a file.
"""
def __init__(self, *args, **kwargs):
"""
Initialize the settings object by either using a file or sepcifying the
settings directly. Works exatly like a dict(), only with extended
capabilities like saving and loading to disk.
"""
try:
self.filename = kwargs.pop('filename')
except KeyError:
print('Creating new settings object.')
else:
print('Loading settings from: "{}".'.format(self.filename))
finally:
super(InversionSettings, self).__init__(*args, **kwargs)
if hasattr(self, 'filename'):
self.update(InversionSettings.loadtxt(self.filename))
def save(self, f):
"""
Saves the settings object to disk.