Merge pull request #45 from jonnymaserati/dev

Added SurveyHeader class and ISCWSA MWD Rev5 error model

README.md

@@ -16,6 +16,7 @@
 
 ## New Features!
 
+  - **ISCWSA MWD Rev5 error model:** add the latest ISCWSA error model that includes tortuousity effects on location uncertainty.
   - **Import from Landmark .wbp files:** using the `exchange.wbp` module it's now possible to import .wbp files exported from Landmark's COMPASS or DecisionSpace software.
   ```python
 import welleng as we
@@ -53,11 +54,19 @@ we.exchange.wbp.save_to_file(doc, "demo.wbp") # save the document to file
 
 [welleng] requires [trimesh], [numpy] and [scipy] to run. Other libraries are optional depending on usage and to get [python-fcl] running on which [trimesh] is built may require some additional installations. Other than that, it should be an easy pip install to get up and running with welleng and the minimum dependencies.
 
+Here's how to get the trickier dependencies manually installed on Ubunut (further instructions can be found [here](https://github.com/flexible-collision-library/fcl/blob/master/INSTALL)):
+
+```python
+sudo apt-get update
+sudo apt-get install libeigen3-dev libccd-dev octomap-tools
+```
+On a Mac you should be able to install the above with brew and on a Windows maching you'll probably have to build these libraries following the instruction in the link, but it's not too tricky. Once the above are installed, then it should be a simple:
+
 ```python
 pip install welleng
 ```
 
-For developers, the repository can be cloned and locally installed in your GitHub directory via your preferred Python env.
+For developers, the repository can be cloned and locally installed in your GitHub directory via your preferred Python env (the `dev` branch is usuall a version or two ahead of the `main`).
 
 ```python
 git clone https://github.com/jonnymaserati/welleng.git
@@ -73,44 +82,52 @@ Here's an example using `welleng` to construct a couple of simple well trajector
 
 ```python
 import welleng as we
-import numpy as np
 from tabulate import tabulate
 
 # construct simple well paths
 print("Constructing wells...")
 connector_reference = we.connector.Connector(
-    pos1=[0,0,0],
-    inc1=0,
-    azi1=0,
-    pos2=[-100,0,2000.],
+    pos1=[0., 0., 0.],
+    inc1=0.,
+    azi1=0.,
+    pos2=[-100., 0., 2000.],
     inc2=90,
     azi2=60,
 ).survey(step=50)
 
 connector_offset = we.connector.Connector(
-    pos1=[0,0,0],
-    inc1=0,
-    azi1=225,
-    pos2=[-280,-600,2000],
-    inc2=90,
-    azi2=270,
+    pos1=[0., 0., 0.],
+    inc1=0.,
+    azi1=225.,
+    pos2=[-280., -600., 2000.],
+    inc2=90.,
+    azi2=270.,
 ).survey(step=50)
 
-# make a survey object and calculate the uncertainty covariances
+# make survey objects and calculate the uncertainty covariances
 print("Making surveys...")
+sh_reference = we.survey.SurveyHeader(
+    name="reference",
+    azi_reference="grid"
+)
 survey_reference = we.survey.Survey(
     md=connector_reference.md,
     inc=connector_reference.inc_deg,
     azi=connector_reference.azi_deg,
-    error_model='ISCWSA_MWD'
+    header=sh_reference,
+    error_model='iscwsa_mwd_rev4'
+)
+sh_offset = we.survey.SurveyHeader(
+    name="offset",
+    azi_reference="grid"
 )
-
 survey_offset = we.survey.Survey(
     md=connector_offset.md,
     inc=connector_offset.inc_deg,
     azi=connector_offset.azi_deg,
-    start_nev=[100,200,0],
-    error_model='ISCWSA_MWD'
+    start_nev=[100., 200., 0.],
+    header=sh_offset,
+    error_model='iscwsa_mwd_rev4'
 )
 
 # generate mesh objects of the well paths
@@ -150,13 +167,14 @@ lines = we.visual.get_lines(clearance_mesh)
 
 # plot the result
 we.visual.plot(
-    [mesh_reference.mesh, mesh_offset.mesh], # list of meshes
-    names=['reference', 'offset'], # list of names
-    colors=['red', 'blue'], # list of colors
+    [mesh_reference.mesh, mesh_offset.mesh],  # list of meshes
+    names=['reference', 'offset'],  # list of names
+    colors=['red', 'blue'],  # list of colors
     lines=lines
 )
 
 print("Done!")
+
 ```
 
 This results in a quick, interactive visualization of the well meshes that's great for QAQC. What's interesting about these results is that the ISCWSA method does not explicitly detect a collision in this scenario wheras the mesh method does.
@@ -172,13 +190,10 @@ Well trajectory generated by [build_a_well_from_sections.py]
 ## Todos
 
  - Add a Target class to see what you're aiming for - **in progress**
- - Export to Landmark's .wbp format so survey listings can be modified in COMPASS - **in progress**
  - Documentation
  - Generate a scene of offset wells to enable fast screening of collision risks (e.g. hundreds of wells in seconds)
- - Well trajectory planning - construct your own trajectories using a range of methods (and of course, including some novel ones) **- DONE!**
- - More error models - **in progress**
+ - More error models - **added the ISCWSA MWD Rev5 error model**
  - WebApp for those that just want answers
- - Viewer - a 3D viewer to quickly visualize the data and calculated results **- DONE!**
 
 It's possible to generate data for visualizing well trajectories with [welleng], as can be seen with the rendered scenes below.
 ![image](https://user-images.githubusercontent.com/41046859/97724026-b78c2e00-1acc-11eb-845d-1220219843a5.png)

examples/build_a_well_from_sections.py

@@ -1,15 +1,15 @@
-import welleng as we
+# import welleng as we
 from welleng.connector import Connector, interpolate_well, get_survey
 from welleng.mesh import WellMesh
 from welleng.visual import plot
 
 # define start position and vector
-pos1 = [0,0,0]
-vec1 = [0,0,1] # this is the same as inc=0, azi=0
+pos1 = [0., 0., 0.]
+vec1 = [0., 0., 1.]  # this is the same as inc=0, azi=0
 
 # for the first section, we want to hold vertical for the first 500m
 md2 = 500
-vec2 = [0,0,1]
+vec2 = [0., 0., 1.]
 
 # let's connect those points
 s1 = Connector(
@@ -37,7 +37,7 @@
 # we want to be near horizontal when we hit this point so that we can
 # drill the reservoir horizontal (let's say 88 deg) and the reseroir
 # orientation is southeast-northwest and we have good directional control
-pos4 = [-800,300,1800]
+pos4 = [-800., 300., 1800.]
 inc4 = 88
 azi4 = 315
 dls_design4 = 4
@@ -53,7 +53,7 @@
 )
 
 # finally, we want a 500m horizontal section in the reservoir
-md5=s3.md_target + 500
+md5 = s3.md_target + 500
 inc5 = 90
 
 s4 = Connector(
@@ -77,6 +77,6 @@
 mesh = WellMesh(survey, method='circle')
 
 # finally, plot it
-plot([mesh.mesh])
+plot([mesh.mesh], interactive=False)
 
 print("Done!")

examples/calibrate_iscwsa_error_example_1.py

@@ -1,98 +1,63 @@
-import numpy as np
-import pandas as pd
-
 import welleng as we
 
 from openpyxl import load_workbook
-from dataclasses import dataclass
 
 # import the ISCWSA standard Excel data
 print("Importing data...")
 try:
     workbook = load_workbook(
         filename="examples/data/error-model-example-mwdrev4-iscwsa-1.xlsx",
-         data_only=True
+        data_only=True
     )
 except:
-    print("Make sure you have a local copy of ISCWSA's Excel file and have updated the location in the code.")
+    print(
+        "Make sure you have a local copy of ISCWSA's Excel file and have"
+        "updated the location in the code."
+    )
+
 sheets = workbook.sheetnames
 model = workbook['Model']
 wellpath = workbook['Wellpath']
 
-
-@dataclass
-class WellHeader:
-    Latitude: float
-    G: float
-    BTotal: float
-    Dip: float
-    Declination: float
-    Convergence: float
-    AzimuthRef: float
-    DepthUnits: str
-    VerticalIncLimit: float
-    FeetToMeters: float
-
-wh = WellHeader(
-    Latitude=wellpath['B2'].value,
-    G = wellpath['B3'].value,
-    BTotal = wellpath['B4'].value,
-    Dip = wellpath['B5'].value,
-    Declination = wellpath['B6'].value,
-    Convergence = wellpath['B7'].value,
-    AzimuthRef = wellpath['B8'].value,
-    DepthUnits = wellpath['B9'].value,
-    VerticalIncLimit = wellpath['B10'].value,
-    FeetToMeters = wellpath['B11'].value
+sh = we.survey.SurveyHeader(
+    latitude=wellpath['B2'].value,
+    G=wellpath['B3'].value,
+    b_total=wellpath['B4'].value,
+    dip=wellpath['B5'].value,
+    declination=wellpath['B6'].value,
+    convergence=wellpath['B7'].value,
+    azi_reference=(
+        'true' if wellpath['B8'].value == 'TRUE'
+        else 'grid' if wellpath['B8'].value == 'GRID'
+        else 'magnetic'
+    ),
+    depth_unit=wellpath['B9'].value,
+    vertical_inc_limit=wellpath['B10'].value,
 )
 
-well_ref_params = dict(
-    Latitude = wh.Latitude,
-    G = wh.G,
-    BTotal = wh.BTotal,
-    Dip = wh.Dip,
-    Declination = wh.Declination,
-    Convergence = wh.Convergence,   
-)
-
-MD = []
-IncDeg = []
-AziDeg = []
-TVD = []
+md = []
+inc = []
+azi = []
 
 for row in wellpath.iter_rows(
     min_row=3,
     max_row=(),
     min_col=5,
-    max_col=9
 ):
-    MD.append(row[0].value)
-    IncDeg.append(row[1].value)
-    AziDeg.append(row[2].value)
-    TVD.append(row[3].value)
-
-survey_deg = np.stack((MD,IncDeg,AziDeg), axis=-1)
-
-IncRad = np.radians(IncDeg)
-AziRad = np.radians(AziDeg)
-AziTrue = AziRad + np.full(len(AziRad), np.radians(wh.Convergence))
-AziG = AziTrue - np.full(len(AziRad), np.radians(wh.Convergence))
-AziMag = AziTrue - np.full(len(AziRad), np.radians(wh.Declination))
+    md.append(row[0].value)
+    inc.append(row[1].value)
+    azi.append(row[2].value)
 
-survey_master = np.stack((MD,IncRad,AziRad), axis=-1)
-TVD = np.array([TVD])
-AziTrue = np.array([AziTrue])
-AziG = np.array([AziG])
-AziMag = np.array([AziMag])
-
-# get error for entire survey
-print("Calculating ISCWSA MWD Rev4 errors...")
-err0 = we.error.ErrorModel(
-    survey=survey_deg,
-    well_ref_params=well_ref_params,
-    AzimuthRef=wh.AzimuthRef,
+s = we.survey.Survey(
+    md=md,
+    inc=inc,
+    azi=azi,
+    header=sh,
+    error_model="iscwsa_mwd_rev4"
 )
 
+err0 = s.err
+
 cov_nev0 = err0.errors.cov_NEVs.T
 
 # print final covariance matrix for each tool
@@ -105,4 +70,4 @@ class WellHeader:
         f'TOTAL:\n{cov_nev0[-1]}'
     )
 
-input("Press Enter to end...")
+input("Press Enter to end...")

examples/connect_two_random_points.py

@@ -6,7 +6,7 @@
 # Some code for testing the connector module.
 
 # Generate some random pairs of points
-pos1 = [0,0,0]
+pos1 = [0., 0., 0.]
 md1 = 0
 
 pos2 = np.random.random(3) * 1000
@@ -79,7 +79,7 @@
 
 # Initialize a connector object and connect the inputs
 section = we.connector.Connector(
-    pos1=[0.,0.,0],
+    pos1=[0., 0., 0],
     vec1=vec1,
     md2=md2,
     pos2=pos2,
@@ -112,7 +112,9 @@
     end_points = np.concatenate(([section.pos2], [section.pos_target]))
 if section.pos3 is not None:
     start_points = np.concatenate((start_points, [section.pos3]))
-    end_points = np.concatenate(([section.pos2], [section.pos3], [section.pos_target]))
+    end_points = np.concatenate(
+        ([section.pos2], [section.pos3], [section.pos_target])
+    )
 lines = Lines(
     startPoints=start_points,
     endPoints=end_points,
@@ -121,7 +123,7 @@
 )
 
 # Add some arrows to represent the vectors at the start and end positions
-scalar=150
+scalar = 150
 arrows = Arrows(
     startPoints=np.array([
         section.pos1,
@@ -150,4 +152,4 @@
     arrows=arrows,
 )
 
-print("Done")
+print("Done")