ondrolexa / apsg Goto Github PK

Doctest or Pytest module can check examples in comments as they are valid Python code.
We can keep examples up to date with tutorial.

Create a new math/physics abstractions with the following classes:

• Vector
• Matrix
• Tensor

The goal is to clean up and speed up the implementation of these basic mathematical objects.

Hi!

I'm trying to plot a large number of poles from a list where each one has a different color, all of them in another list, however, i'm getting an error that the list of colors "is not a valid value for color". The code i'm trying is:

color_list = [list_of_colors]
g = [list_of_poles]

s.pole(g,color=color_list,ms=7)

And i get the error color_list is not a valid value for color

I can do, alternatively:

s.pole(g[i],color=color_list[i],ms=7) for i in range(len(g))

And works perfect, but it takes waaay longer. I'm guessing i'm missing something in the color input format to make it take a list. Any advice?

Use the master branch as the main development branch. Using a develop branch complicates the development process. When you use the develop branch all the hot-fixes have to be merged back from master to develop. There is also no project activity visible to the repository visitors (potential contributors) unless we merge the develop back to master, which happens not so often. At least merging to the master force us to be more critical when we write or review a new code.

• http://endoflineblog.com/oneflow-a-git-branching-model-and-workflow
• https://www.toptal.com/software/trunk-based-development-git-flow

Hi @ondrolexa

I am currently trying to split the Structure Name into it's separated groups but have no success. Would you be able to suggest a solution?

s=StereoNet()

test_list=[]
for i in vein_names:
    for index in range(len(vein_names)):
        vein_df = []
        test =sg_data.loc[sg_data['Structure Name'] == i]
        test
        sg_vein = Group.from_array(azis = test['Dip Direction (TN)'], 
                    incs = test['Dip'], 
                    typ=Fol , 
                    name=i)
        s.pole(sg_vein,label= i)
s.pole(sg_vein,label= i)
s.contourf(sg_vein, 20, legend=True, sigma=2)
s.show()

I have a problem when I use this library. I want to see the stereonet diagram but there is an error when I run the program (the error is seen in the image). Please, can someone help me with this problem?

thanks!

Will there be Polar plotting of stereonets added in the near future?

Hello!

Sorry if this is not the proper section for questions, but i wanted to ask.. it's possible to calculate the safety factor of a wedge failure planes and the corresponding slope using apsg?

Thanks in advance!

Hi!
I sought to pull data from an rs3 file to perform further computations by using the from_rs3 class method. In this rs3 file, values for 'BDec' and 'BInc' are not specified.
Here's the code I used:

from apsg.feature import Core
rs3path = '/content/drive/MyDrive/paleomagnetism/2-1.rs3'
rs3core = Core.from_rs3(rs3path)
rs3core.datatable()

Upon running my code, an AttributeError pops up, stating that "AttributeError: 'NoneType' object has no attribute 'dd' ".
And the full error message can be seen below:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-3-53bbc95bbeba> in <cell line: 4>()
      2 rs3path = '/content/drive/MyDrive/paleomagnetism/2-1.rs3'
      3 rs3core = Core.from_rs3(rs3path)
----> 4 rs3core.datatable()

1 frames
/usr/local/lib/python3.10/dist-packages/apsg/feature/_paleomag.py in tilt(self)
    400         """Returns ``Vector3Set`` of vectors in tilt‐corrected coordinates system"""
    401         return self.geo.rotate(
--> 402             Lineation(self.bedding.dd[0] - 90, 0), -self.bedding.dd[1]
    403         )
    404 

AttributeError: 'NoneType' object has no attribute 'dd'

Hence, I modified the code as follows:

from apsg import fol
from apsg.feature import Core
rs3path = '/content/drive/MyDrive/paleomagnetism/2-1.rs3'
rs3core = Core.from_rs3(rs3path)
rs3core.bedding = fol(0,0)
rs3core.datatable()

However, this time, an AttributeError arises again, stating that "AttributeError: 'Foliation' object has no attribute 'dd' ".
And here is the full error message produced by running the modified code as follows:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-4-2849371bd677> in <cell line: 6>()
      4 rs3core = Core.from_rs3(rs3path)
      5 rs3core.bedding = fol(0,0)
----> 6 rs3core.datatable()

1 frames
/usr/local/lib/python3.10/dist-packages/apsg/feature/_paleomag.py in tilt(self)
    400         """Returns ``Vector3Set`` of vectors in tilt‐corrected coordinates system"""
    401         return self.geo.rotate(
--> 402             Lineation(self.bedding.dd[0] - 90, 0), -self.bedding.dd[1]
    403         )
    404 

AttributeError: 'Foliation' object has no attribute 'dd'

Could you provide some advice on how to solve this? Your assistance would be greatly appreciated.

Write tests for IPython notebooks to be sure that they are always evaluated and synchronized with the code base.

We can use this plugin: https://github.com/computationalmodelling/nbval

this is my code that plots normal Rose Diagram using PDF method:

import pandas as pd

from apsg import *
from apsg.feature import Vector2Set as vec2set
from apsg.helpers._notation import *
from apsg.plotting._roseplot import *

##### ROSE DIAGRAM ######
# read data from CSV file
df = pd.read_csv('../test-stereonet-anticline1.csv')

# create a list of 2D vectors from the data
vectors2 = [vec2((sind(x - 90) * cosd(y)), (cosd(x + 90) * cosd(y))) for x, y in zip(df['DipD'], df['Dip'])]

# create a Vector2Set object from the list of vectors
vs1 = vec2set(vectors2)

p = RosePlot(grid=True, title='Test Rose Diagram',
             bins=36, axial=True,
             density=True, kappa=250,
             scaled=False, ticks=True,
             arrowness=0.95, rwidth=1,
             pdf_res=1000, cmap="jet")

p.pdf(vs1, fc='White', ec='Blue', ls="-", lw=1, legend=True)
p.show()

the output is like the first photo that is drawn in Blue

and a second code that does plot each shape individually using this code:

import pandas as pd
from apsg import *
from apsg.feature import Vector2Set as vec2set
from apsg.helpers._notation import *
from apsg.plotting._roseplot import *
from sklearn.cluster import KMeans

##### ROSE DIAGRAM ######

# read data from CSV file
df = pd.read_csv('../test-stereonet-anticline1.csv')

# Add k-means clustering
clust = 5
kmeans = KMeans(n_clusters=clust, n_init="auto", random_state=0)
kmeans.fit(df)
centers = kmeans.cluster_centers_
SD = [(centers[i][0], centers[i][1]) for i in range(clust)]
colors = ['red', 'green', 'blue', 'orange', 'purple']

p = RosePlot(grid=True, title='Test Rose Diagram',
             bins=36, axial=True,
             density=True, kappa=250,
             scaled=False, ticks=False,
             arrowness=0, rwidth=1,
             pdf_res=1000)

for i, center in enumerate(SD):
    vectors = []
    vector2 = [vec2((sind(center[0] - 90) * cosd(center[1])), (cosd(center[0] + 90) * cosd(center[1])))]
    vectors.extend(vector2)
    vs = vec2set(vectors)
    p.pdf(vs, fc='White', ec=colors[i], ls="-", lw=1, label=f'Cluster {i+1}')

p.show() 

and the output is the second photo that has different colors:

Here is the Issuse

I want those shapes completely separated so that i can set each one a new color meanwhile i want them to be scaled just like the first one.

and Idea on how to integrate this?

My input data is some folded beddings in righ hand rule format (ignore the header please) and it's it attached as well.

test-stereonet-anticline1.csv

Regards
Nima

Hello Again,
I wonder if there is any way to plot focal mechanism using APSG lib, It can simply be done by OBSPY by giving Strike, Dip, Rake but have focal mechanism meanwhile PTB Axis and other statistical methods wil be great.
If not i would be happy to help implementing that,
Regards

It would be nice to manage dependencies via pipenv instead of requirements.txt files. The reason is that you have automatic virtualenv management, deterministic install/uninstall of dependencies and so on.
https://docs.pipenv.org/

(... I thing this is a package or library: "Structural geology module for Python". ?)

Numpy and Pandas will drop the support for Python 2.

Pandas: Starting January 1, 2019, pandas feature releases will support Python 3 only. See Plan for dropping Python 2.7 for more.
Numpy: Starting on January 1, 2019, any new feature releases will support only Python3.

If we will remove the Python 2 support wen can use more Python 3 features as typing annotations and dataclasses (new in 3.7).

Hi, Ondrej

I can't run following example from the tutorial:

g1 = Group.randn_lin(mean=Lin(45, 30))
g2 = Group.randn_lin(mean=Lin(320, 56))
g3 = Group.randn_lin(mean=Lin(150, 40))
g = g1 + g2 + g3
cl = Cluster(g)   # <==== error
cl.dendrogram(no_labels=True)

traceback:

AttributeError                            Traceback (most recent call last)
<ipython-input-14-90e135d9136a> in <module>()
----> 1 import codecs, os;__pyfile = codecs.open('''/tmp/py32407pTR''', encoding='''utf-8''');__code = __pyfile.read().encode('''utf-8''');__pyfile.close();os.remove('''/tmp/py32407pTR''');exec(compile(__code, '''/home/jw/work/apsg_tutorial.py''', 'exec'));

/home/jw/work/apsg_tutorial.py in <module>()
----> 1 # APSG defines several new python classes to easily manage, analyze and
      2 # visualize orientation structural geology data.Base class Vec3 is derived from
      3 # numpy.array class and offers several new method which will be explained in
      4 # following examples
      5 

/home/jw/.virtualenvs/scienv/lib/python2.7/site-packages/apsg/core.pyc in __init__(self, d, **kwargs)
   2069     def __init__(self, d, **kwargs):
   2070         assert isinstance(d, Group), 'Only group could be clustered'
-> 2071         self.data = Group(d.copy())
   2072         self.maxclust = kwargs.get('maxclust', 2)
   2073         self.angle = kwargs.get('angle', None)

/home/jw/.virtualenvs/scienv/lib/python2.7/site-packages/apsg/core.pyc in copy(self)
    856 
    857     def copy(self):
--> 858         return Group(super(Group, self).copy(), self.name)
    859 
    860     @property

AttributeError: 'super' object has no attribute 'copy'

System

Linux Mint 18.3
Python 2.7.12

scipy==1.0.1
numpy==1.14.2
matplotlib==2.2.2
apsg==0.5.1

Hi!
When i add a column of points/planes to a pandas dataframe, they are not shown when printing the dataframe in the "compact" format they usually have when you single print them but rather as an array of points (example in the picture below).

Is there any way to "force" pandas to show the lines/planes in that compact 'dipdir/dip' format in the dataframes?

Hello Ondrej,

Is it possible to add right hand rule notation to the StereoNet class? I plotted some data and now I can't change the notation displayed in the legend.

Structural geology package for Python

It's possible to, somehow, get the resulting parameters/centroids/density values from a density contour analysis/plot for a set of poles?

I'm guessing it uses Kamb.