loop3d / dh2loop

A package to extract information from drillholes to feed 3D modelling packages

Loop Documentation

Loop Project Website

What is Loop?

The Loop platform is an open source 3D probabilistic geological and geophysical modelling platform, initiated by Geoscience Australia and the OneGeology consortium. The project is funded by Australian territory, State and Federal Geological Surveys, the Australian Research Council and the MinEx Collaborative Research Centre.

What does the Loop GUI do?

This GUI makes using Loop python packages easier. Incorporating map2loop and LoopStructural into a basic interface. This enables the user to select a region of interest from a simple map interface, run map2loop to extract a geological event history and observation data, and then create a 3D model of the subsurface of that region using LoopStructural. An area of 100x100km takes a little under 10 minutes from start to finish.

Additionally the GUI allows the user to correct data or remove extracted data that is believed to be erroneous and change options for running the modelling scripts. This enables the user to quickly try different conceptual models of how the region geologically formed.

Licencing

The Loop3D GUI repository is under the LGPL license

dh2loop's Issues

Add pip install

set version number in setup.py, both for version and in download_url, also in the config file of the documentation

version='X.X',
download_url='https://github.com/cgre-aachen/gempy/archive/X.X.tar.gz',

add new tag

$ git tag X.X -m "Add X.X tag for PyPI"

push git tag

$ git push --tags origin master

upload newest version to PyPi

First create the dist

python3 setup.py sdist bdist_wheel

Second upload the distributions

twine upload dist/*

Download timeout

Just trying out the report download notebook

Bounds: (122.088628, -26.019766, 123.846735, -24.988548)
---------------------------------------------------------------------------
TimeoutError                              Traceback (most recent call last)
File ~/anaconda3/envs/xarray/lib/python3.8/urllib/request.py:1354, in AbstractHTTPHandler.do_open(self, http_class, req, **http_conn_args)
   1353 try:
-> 1354     h.request(req.get_method(), req.selector, req.data, headers,
   1355               encode_chunked=req.has_header('Transfer-encoding'))
   1356 except OSError as err: # timeout error

File ~/anaconda3/envs/xarray/lib/python3.8/http/client.py:1256, in HTTPConnection.request(self, method, url, body, headers, encode_chunked)
   1255 """Send a complete request to the server."""
-> 1256 self._send_request(method, url, body, headers, encode_chunked)

File ~/anaconda3/envs/xarray/lib/python3.8/http/client.py:1302, in HTTPConnection._send_request(self, method, url, body, headers, encode_chunked)
   1301     body = _encode(body, 'body')
-> 1302 self.endheaders(body, encode_chunked=encode_chunked)

File ~/anaconda3/envs/xarray/lib/python3.8/http/client.py:1251, in HTTPConnection.endheaders(self, message_body, encode_chunked)
   1250     raise CannotSendHeader()
-> 1251 self._send_output(message_body, encode_chunked=encode_chunked)

File ~/anaconda3/envs/xarray/lib/python3.8/http/client.py:1011, in HTTPConnection._send_output(self, message_body, encode_chunked)
   1010 del self._buffer[:]
-> 1011 self.send(msg)
   1013 if message_body is not None:
   1014 
   1015     # create a consistent interface to message_body

File ~/anaconda3/envs/xarray/lib/python3.8/http/client.py:951, in HTTPConnection.send(self, data)
    950 if self.auto_open:
--> 951     self.connect()
    952 else:

File ~/anaconda3/envs/xarray/lib/python3.8/http/client.py:922, in HTTPConnection.connect(self)
    921 """Connect to the host and port specified in __init__."""
--> 922 self.sock = self._create_connection(
    923     (self.host,self.port), self.timeout, self.source_address)
    924 self.sock.setsockopt(socket.IPPROTO_TCP, socket.TCP_NODELAY, 1)

File ~/anaconda3/envs/xarray/lib/python3.8/socket.py:808, in create_connection(address, timeout, source_address)
    807 try:
--> 808     raise err
    809 finally:
    810     # Break explicitly a reference cycle

File ~/anaconda3/envs/xarray/lib/python3.8/socket.py:796, in create_connection(address, timeout, source_address)
    795     sock.bind(source_address)
--> 796 sock.connect(sa)
    797 # Break explicitly a reference cycle

TimeoutError: [Errno 110] Connection timed out

During handling of the above exception, another exception occurred:

URLError                                  Traceback (most recent call last)
Input In [7], in <cell line: 2>()
      1 bounds=GeoJSON(data=dc.last_draw)
----> 2 wamex.get_reports (bounds)

File ~/.local/lib/python3.8/site-packages/dh2loop-0.0.1-py3.8.egg/dh2loop/wamex.py:189, in get_reports(bounds)
    185 """
    186 Downloads reports from a defined region
    187 """
    188 bbox, bbox2, bounds2 =define_bounds(bounds)
--> 189 anumberscode=query_anumbers(bbox, bbox2, bounds2)
    190 if not anumberscode:
    191     print ("No reports available in this region")

File ~/.local/lib/python3.8/site-packages/dh2loop-0.0.1-py3.8.egg/dh2loop/wamex.py:90, in query_anumbers(bbox, bbox2, bounds2)
     88 try:
     89     collars_file='http://geo.loop-gis.org/geoserver/loop/wfs?service=WFS&version=1.0.0&request=GetFeature&typeName=loop:collar_4326&bbox='+bbox2+'&srs=EPSG:4326'
---> 90     collars = gpd.read_file(collars_file, bbox=bbox)
     91     print("Connected to Loop Server")
     92     anumbers=gpd.GeoDataFrame(collars, columns=["anumber"])

File ~/anaconda3/envs/xarray/lib/python3.8/site-packages/geopandas/io/file.py:242, in _read_file(filename, bbox, mask, rows, engine, **kwargs)
    240 from_bytes = False
    241 if _is_url(filename):
--> 242     req = _urlopen(filename)
    243     path_or_bytes = req.read()
    244     from_bytes = True

File ~/anaconda3/envs/xarray/lib/python3.8/urllib/request.py:222, in urlopen(url, data, timeout, cafile, capath, cadefault, context)
    220 else:
    221     opener = _opener
--> 222 return opener.open(url, data, timeout)

File ~/anaconda3/envs/xarray/lib/python3.8/urllib/request.py:525, in OpenerDirector.open(self, fullurl, data, timeout)
    522     req = meth(req)
    524 sys.audit('urllib.Request', req.full_url, req.data, req.headers, req.get_method())
--> 525 response = self._open(req, data)
    527 # post-process response
    528 meth_name = protocol+"_response"

File ~/anaconda3/envs/xarray/lib/python3.8/urllib/request.py:542, in OpenerDirector._open(self, req, data)
    539     return result
    541 protocol = req.type
--> 542 result = self._call_chain(self.handle_open, protocol, protocol +
    543                           '_open', req)
    544 if result:
    545     return result

File ~/anaconda3/envs/xarray/lib/python3.8/urllib/request.py:502, in OpenerDirector._call_chain(self, chain, kind, meth_name, *args)
    500 for handler in handlers:
    501     func = getattr(handler, meth_name)
--> 502     result = func(*args)
    503     if result is not None:
    504         return result

File ~/anaconda3/envs/xarray/lib/python3.8/urllib/request.py:1383, in HTTPHandler.http_open(self, req)
   1382 def http_open(self, req):
-> 1383     return self.do_open(http.client.HTTPConnection, req)

File ~/anaconda3/envs/xarray/lib/python3.8/urllib/request.py:1357, in AbstractHTTPHandler.do_open(self, http_class, req, **http_conn_args)
   1354         h.request(req.get_method(), req.selector, req.data, headers,
   1355                   encode_chunked=req.has_header('Transfer-encoding'))
   1356     except OSError as err: # timeout error
-> 1357         raise URLError(err)
   1358     r = h.getresponse()
   1359 except:

URLError: <urlopen error [Errno 110] Connection timed out>

Adding PVgeo-pyvista visualization

Adding a pyvista render to see the borehole data in place - called directly from a notebook.

Here there is an example how to plot tubes in PVgeo:

https://pvgeo.org/examples/filters-general/points-to-tube.html#sphx-glr-examples-filters-general-points-to-tube-py