Utility program: add all images in your directory to make a video

 

If you want to add all the images in your directory sequentially to make a video for a presentation then you can use this utility program.

In the first step, we will make a series of “.png” images by plotting the bar diagram of the GDP of the top 10 countries with years (1960-2017). We then add all these images sequentially to make a video. Here, we will add the images using the cv2 package of Python. Please keep in mind that the video can also be created using the matplotlib package of python. This is an alternative to perform the same task. In some cases, when we have a collection of images and we want to add them, then also this can be very handy.

To install the cv2 package using Anaconda, type:

conda install -c menpo opencv

Now, we can obtain the data for GDP of all countries from 1960-2017 from the World Bank website. We then use “pandas” package of Python to read the csv data file and “matplotlib” package to plot the bar diagram.

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib.ticker import FuncFormatter

# function for setting the format of values in billions of dollars
def trillions(x,pos):
    'The two args are the value and tick position'
    return '${:.1f}T'.format(x * 1e-12)
formatter = FuncFormatter(trillions)

df=pd.read_csv('API_NY.GDP.MKTP.CD_DS2_en_csv_v2_10203569.csv',skiprows=3)
df = df.set_index("Country Name")
with open('neglect_regions.txt',mode='r') as file:
    alist = [line.rstrip() for line in file]
# print(alist)
df=df.drop(alist)

years=np.arange(1960,2018)
xx=45
for year in years:
    num=10
    print(year)
    top_10=df.nlargest(num, str(year))
    # print(top_10[str(year)])
    fig, ax = plt.subplots(figsize=(10,6))
    ax.yaxis.set_major_formatter(formatter)
    plt.bar(np.arange(num),top_10[str(year)].values)
    plt.xticks(np.arange(num), top_10.index.values,fontsize=6)
    plt.title(str(year))
    plt.savefig('figures/gdprank_{}.png'.format(year),dpi=200,bbox_inches='tight')
    plt.close(fig) #to clear the memory
    plt.cla()

#source:https://data.worldbank.org

 

gdprank_2017.png

The series of bar diagram for each year from 1960-2017 is saved in the “figures” directory. Then we can run the command:

python conv_image2video.py -loc "figures" -o "world_countries_gdp.mp4"

to add all the “.png” images in the figures directory to make the video named “world_countries_gdp.mp4”.

Usage of the program “conv_image2video.py”

  1. To convert the images in the current directory, with the extension “.png”, output file name “output.mp4” and frame rate 5 fps, simply type:

python conv_image2video.py

  1. If you want to change some options, add the following flags:
-loc "path_to_images": This will look for images in the directory "path_to_images"; default="."
-o "custom_name.mp4": This will output the video with the name "custom_name.mp4"; default: "output.mp4"
-ext "jpg": This will work on the jpeg images; default: "png"
-fr "1": This will change the speed/frame rate of the video; default: "5"

 

To download this program, click here.

If you want to download all the files (program +examples), click here.

Working with MATLAB & Python simultaneously and smoothly​

MATLAB and Python are both well known for its usefulness in the scientific computing world. There are several advantages of using one over another. Python is preferable for most of the programmers because it’s free, beautiful, and powerful. MATLAB, on the other hand, has advantages like there is the availability of a solid amount of functions, and Simulink. Both the languages have a large scientific community and are easier to learn for the beginners. Though MATLAB, because it includes all the packages we need is easier to start with than the Python where we need to install extra packages and also require an IDE. The proprietary nature of the algorithms in MATLAB i.e., we cannot see the codes of most of the algorithms and we have to trust them to implement for our usage makes us sometimes hard to prefer MATLAB over the other options available like Python. Besides, these proprietary algorithms of MATLAB come at a cost!

In short, in order to excel in all of our scientific tasks, we need to learn to utilize both of them interchangeably. This is where the Python’s module SciPy comes in handy. MATLAB reads its proprietary “mat” data format quite efficiently and fastly. The SciPy’s module, “loadmat” and “savemat” can easily read and write the data stored in the Python variable into the “mat” file, respectively. Here, we show an example to use the data from MATLAB in the “mat” format to plot in Python on a geographical map, which Python can execute much efficiently than MATLAB.

Saving the MATLAB variables into a “mat” file

In this example MATLAB script, we show how can we read the “mat” file in the MATLAB script and save it.

clear; close all; clc 

%% Load the two matfiles with some data into the workspace
load python_export_CME_ATML_orig_vars;
load station_info;

%% Remove the unrequired variables from the MATLAB's memory 
clearvars slat slon;

%% Saving the data from the "station_info.mat" file as a cell data type
stns={slons' slats' stn_name'}; 

%% Conduct some operations with the data and save it in "admF" variable
admF=[]; %intializing the matrix
std_slU=std(slU);
for i=1:length(slons)
    ccU=corrcoef(dU(:,i),slU); %Making use of the available MATLAB functions
    std_dU=std(dU(:,i));
    admF=[admF ccU(1,2)*(std_dU/std_slU)];
end

%% Saving the output "admF" matrix into the "MATLAB_export_admittance_output.mat" file at a desired location.
save('../EOF_python/MATLAB_export_admittance_output.mat','admF')

Using the data from the “mat” file in Python to plot on a geographical map

import scipy.io as sio #importing the scipy io module for reading the mat file
import numpy as np #importing numpy module for efficiently executing numerical operations
import matplotlib.pyplot as plt #importing the pyplot from the matplotlib library
from mpl_toolkits.basemap import Basemap #importing the basemap to plot the data onto geographical map
from matplotlib import rcParams
rcParams['figure.figsize'] = (10.0, 6.0) #predefine the size of the figure window
rcParams.update({'font.size': 14}) # setting the default fontsize for the figure
from matplotlib import style
style.use('ggplot') # I use the 'ggplot' style for plotting. This is optional and can be used only if desired.

# Change the color of the axis ticks
def setcolor(x, color):
     for m in x:
         for t in x[m][1]:
             t.set_color(color)

# Read the two mat files and saving the MATLAB variables as the Python variables
ADF = sio.loadmat('MATLAB_export_admittance_output.mat')
admF=np.array(ADF['admF'])[0]

STN = sio.loadmat('station_info.mat')
slon=np.array(STN['slons'])[0]
slat=np.array(STN['slats'])[0]

## Converting MATLAB cell type to numpy array data type
stnname=np.array(STN['stn_name'])[0]
sname=[]
for ss in stnname:
    sname.append(ss[0])
sname=np.array(sname)

## Plotting the admittance values
plt.figure()
offset=0.5
m = Basemap(llcrnrlon=min(slon)-offset,llcrnrlat=min(slat)-offset,urcrnrlon=max(slon)+offset,urcrnrlat=max(slat)+offset,
        projection='merc',
        resolution ='h',area_thresh=1000.)
xw,yw=m(slon,slat) #projecting the latitude and longitude data on the map projection

m.drawmapboundary(fill_color='#99ffff',zorder=0) #plot the map boundary
m.fillcontinents(color='w',zorder=1) #fill the continents region
m.drawcoastlines(linewidth=1,zorder=2) #draw the coastlines
# draw parallels
par=m.drawparallels(np.arange(21,26,1),labels=[1,0,0,0], linewidth=0.0)
setcolor(par,'k') #The color of the latitude tick marks has been set to black (default) but can be changed to any desired color
# draw meridians
m.drawmeridians(np.arange(120,123,1),labels=[0,0,0,1], linewidth=0.0)

cax=m.scatter(xw,yw,c=admF,zorder=3,s=300*admF,alpha=0.75,cmap='viridis') #plotting the data as a scatter points on the map
cbar = m.colorbar(cax) #plotting the colorbar
cbar.set_label(label='Estimated Admittance Factor',weight='bold',fontsize=16) #customizing the colorbar
plt.savefig('all_stations_admittance.png',dpi=200,bbox_inches='tight') #saving the best cropped output figure as a png file with resolution of 200 dpi.

Output figure from Python

all_stations_admittance

Plot geochemical data using python: An example of analyzing Adakite rock data from GEOROC

We download the precompiled data of adakite from GEOROC database.
For a simple impression of adakite, the wikipedia page gives some clue: Adakites are volcanic rocks of intermediate to felsic composition that have geochemical characteristics of magma thought to have formed by partial melting of altered basalt that is subducted below volcanic arcs.

In this example, we demonstrate how to use python to simplify the data, discard the null data, classify and plot the geochemical properties.

First, let’s look at the data, it is quite large and differs in the available data: some elements are there, some are not.

Screen Shot 2018-09-24 at 3.50.03 PM

Now we can start by importing some useful packages:

import pandas as pd
import matplotlib.pyplot as plt
from mpl_toolkits.basemap import Basemap
import warnings
warnings.filterwarnings("ignore")
plt.rcParams['figure.figsize'] = (20, 10)
plt.style.use('default')

We use pandas to import the data, the encoding is used to solve some font conflicts.

df = pd.read_csv("ADAKITE.csv", encoding="iso-8859-1")

We use dropna() method to discard columns with less than 50% data available.

df = df.dropna(axis=1, thresh=int(0.5*len(df)))

To have a look at the sample occurrence, let’s plot the data. We select the lon, lat column, drop null value and change all data to numeric format.

plt.figure(figsize=(10,10))
m = Basemap(lon_0=180,projection='hammer')
lon = df["LONGITUDE MIN"].dropna()
lat = df["LATITUDE MIN"].dropna()
lon = pd.to_numeric(lon, errors='ignore');
lat = pd.to_numeric(lat, errors='ignore');
lon_ = [];lat_ = []
for x, y in zip(lon,lat):
    try:
        xx, yy = m(float(x),float(y))
        lon_.append(xx);lat_.append(yy)
    except:
        pass
m.scatter(lon_, lat_, marker = "o" ,s=15, c="r" , edgecolors = "k", alpha = 1)
m.drawcoastlines()
plt.title('Adakite rocks sample')
plt.show()

download

We make a function called plot_harker() to plot Harker’s diagram:

def plot_harker(x,xlabel,y,ylabel,title=None,xlim=[40,80],ylim=None,color = "b",label=None):
    plt.scatter(x=x,y=y,marker="o", c=color,s=8,label = label)
    plt.xlabel(xlabel)
    plt.ylabel(ylabel)
    plt.xlim(xlim)
    try:
        plt.ylim(ylim)
    except:
        pass
    if title != None:
        plt.title(title)

… and then plot some elements using that function:

plt.figure(figsize=(12,12))
plt.subplot(321)
plot_harker(x=df["SIO2(WT%)"],xlabel=r'$SiO_2$ (wt%)',
            y=df["AL2O3(WT%)"],ylabel=(r'$Al_2O_3$ (wt%)'),title=r'$SiO_2$ vs $Al_2O_3$')
plt.subplot(322)
plot_harker(x=df["SIO2(WT%)"],xlabel=r'$SiO_2$ (wt%)',
            y=df["MGO(WT%)"],ylabel=(r'$MgO$ (wt%)'),title=r'$SiO_2$ vs $MgO$')
plt.subplot(323)
plot_harker(x=df["SIO2(WT%)"],xlabel=r'$SiO_2$ (wt%)',
            y=df["FEOT(WT%)"],ylabel=(r'$FeOt$ (wt%)'),title=r'$SiO_2$ vs $FeOt$')
plt.subplot(324)
plot_harker(x=df["SIO2(WT%)"],xlabel=r'$SiO_2$ (wt%)',
            y=df["TIO2(WT%)"],ylabel=(r'$TiO_2$ (wt%)'),title=r'$SiO_2$ vs $TiO_2$')
plt.subplot(325)
plot_harker(x=df["SIO2(WT%)"],xlabel=r'$SiO_2$ (wt%)',
            y=df["NA2O(WT%)"],ylabel=(r'$Na_2O$ (wt%)'),title=r'$SiO_2$ vs $Na_2O$')
plt.subplot(326)
plot_harker(x=df["SIO2(WT%)"],xlabel=r'$SiO_2$ (wt%)',
            y=df["K2O(WT%)"],ylabel=(r'$MgO$ (wt%)'),title=r'$SiO_2$ vs $K_2O$')
plt.suptitle(r'Harker diagram of Adakite vs $SiO_2$',y=0.92,fontsize=15)
plt.subplots_adjust(hspace=0.3)
plt.show()

download (1).png

We can try to see the tectonic settings of the rock:

plt.figure(figsize=(8,8))
tec = df['TECTONIC SETTING'].dropna()
tec = tec.replace('ARCHEAN CRATON (INCLUDING GREENSTONE BELTS)','ARCHEAN CRATON')
tec_counts = tec.value_counts()
tec_counts.plot(kind="bar",fontsize=10)
plt.title('Tectonic settings of Adakite')
plt.ylim([0,500])
plt.show()

download (2)

The following code demonstrates how to create new columns and divide the data. We divide the data in High Silica Adakite (SiO2 > 60%) and Low Silica Adakite (SiO2 < 60%)

df['SR/Y'] = (df["SR(PPM)"]/df["Y(PPM)"])
df['CAO+NA2O'] = df['CAO(WT%)'] + df['NA2O(WT%)']
df['CR/NI'] = df['CR(PPM)'] + df['NI(PPM)']
df_hsa = df[df["SIO2(WT%)"] > 60]
df_lsa = df[df["SIO2(WT%)"] < 60]

download (3).png

Bonus: Let’s see the publish about adakite in the GEOROC database by year:

cite = [df.CITATIONS[x] for x in range(0,len(df)) if len(df.CITATIONS[x]) > 20 and df.CITATIONS[x].count('[') < 3]
year = []
for i in range(0,len(cite)):
    year.append(int(cite[i].split('[')[2].split(']')[0]))

download (4)

The python code below is the full program of this example:

Nguyen Cong Nghia
IESAS

Plot seismogram (SAC file), events, stations in Python (Part 1)

Here is an example of plotting SAC files in Python. The sample SAC files can be downloaded here and the Jupyter notebook can be downloaded here.

First, import some useful packages, including obspy, pandas, numpy and Basemap. By the way, they are all great packages (obspy is amazing for anyone who uses seismic data)

from obspy import read
import pandas as pd
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import numpy as np

#Ignore warnings due to python 2 and 3 conflict
import warnings
warnings.filterwarnings("ignore")

Let’s read the sample Z component using read from obspy

stream = read("2015.0529.0700/*Z.sac")

In here, we use the header from SAC file using tr.stats.sac.(SAC_header)

plt.figure(figsize=(10,5))
# setup mercator map projection.
m = Basemap(lon_0=180,projection='hammer')
evlat = stream[0].stats.sac.evla; evlon = stream[0].stats.sac.evlo

#Plot the event
xx,yy = m(evlon,evlat)
m.scatter(xx, yy, marker = "*" ,s=150, c="r" , edgecolors = "k", alpha = 1)

for tr in stream:
    stlat = tr.stats.sac.stla; stlon = tr.stats.sac.stlo 
    m.drawgreatcircle(stlon,stlat,evlon,evlat,linewidth=1,color='b')
    xx,yy = m(stlon,stlat)
    m.scatter(xx, yy, marker = "^" ,s=150, c="g" , edgecolors = "k", alpha = 1)
    
m.drawcoastlines()
#m.fillcontinents()
m.drawparallels(np.arange(-90,90,20),labels=[1,1,0,1])
plt.title("Event-station map")
plt.show()
fig1

I used a simple trick to plot the seismogram with distance by make the y:
y = data + dist*weight_factor
with data is the amplitude of seismic trace, dist: distance in km (SAC header) and weight_factor = 0.01

The red line indicate the predicted P arrival time that I have calculated and store in SAC header t3

plt.figure(figsize=(10,5))
for tr in stream:
    tr.normalize()
    dist = tr.stats.sac.dist
    plt.plot(tr.times(),tr.data+dist*0.01,c="k",linewidth=0.5)
    plt.scatter(tr.stats.sac.t3,dist*0.01,marker="|",color="r")
plt.ylabel("x100 km")    
plt.ylim(84,77)
plt.xlim(650,800)
plt.show()
fig2.png
Plot the same seismogram but using filled colors (which is more suitable to plot other kind of seismic traces)
plt.figure(figsize=(10,5))
for tr in stream:
    tr.normalize()
    dist = tr.stats.sac.dist*0.01
    x = tr.times()
    y = tr.data+dist
    plt.fill_between(x,y, dist, y > dist, color='r', alpha = 0.8)
    plt.fill_between(x,y, dist, y < dist, color='b', alpha = 0.8)
plt.ylabel("x100 km")    
plt.ylim(84,77)
plt.xlim(650,800)
plt.show()
fig3.png
Nguyen Cong Nghia
IESAS

Time-series Analysis using Python I

Introduction

Time-series analysis is essential in most fields of science including geophysics, economics, etc. Most of the geophysical data comes in a time-series format including the seismic recordings. In this part of the series of tutorial, we will see how we can quickly load the data, and visualize it.

Prerequisites

This tutorial does not require the reader to have any basic understanding of Python or any programming language. But we expect the reader to have installed the jupyter notebook on their system. If the reader has not installed it yet, then they can follow the previous post where we went through the steps involved in getting started with Python.

What is Time-series?

Time-series is a collection of data at fixed time intervals. This can be analyzed to obtain long-term trends, statistics, and many other sorts of inferences depending on the subject.

Data

We also need some data to undergo the analysis. We demonstrate the analysis using our GPS data. It can be downloaded from here.

Let’s get started

The first step is always to start the Python interpreter. In our case, we will use the jupyter notebook.

Jupyter notebook can be started using the terminal. Firstly, navigate to your directory containing the data and the type “jupyter notebook” on your terminal.

jupyter notebook

Next, we create a new Python 3 notebook, rename it as pythontut1. Then, we need to import some of the libraries:

import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
from matplotlib.pyplot import rcParams
rcParams['figure.figsize'] = 15, 6

Loading the data

Now, we load the data using the pandas library functions. Here, we use the function read_csv. But, before that let’s observe the format of the data:

!head 0498.COR

The prefix “!” can be used to execute any Linux command in the notebook.

We can see that the data has no header information, and 8 columns. The columns are namely, “year”, “latitude”, “longitude”, “Height”, “dN”, “dE”, “dU”.

So, now we read the data and set the above names to the different columns.

df=pd.read_csv("0498.COR", header=None, delimiter='\s+', names=['Year',"Lat","Long","Hgt","dN","dE","dU","nav"])
df.head()

It is essential to understand the above command. We gave the argument of the filename, header (default is the first line), delimiter (default is a comma) and the names of each column, respectively. Then we output the first 5 lines of the data using the df.head() command.

Our data is now loaded, and if we want to extract any section of the data, we can easily do that.

df['Year'].head()
df[['Year','Lat']].head()

Here, we have used the column names to extract the two columns only. We can also use the index values.

df.loc[:,"Year"].head()
df.iloc[:,3].head()

When we use “.loc” method to extract the section of the data, then we need to use the column name whereas when we use the “.iloc” method then we use the index values. Here, df.iloc[:,3] extracts all the rows of the 3rd column (“Hgt”).

Analysis

Now, we have the data loaded. Let’s plot the “dN”, “dE”, and “dU” values versus the year. Before doing that, let’s set the “Year” column as the index column.

df.set_index("Year", inplace=True)
df.head()

We can see the “Year” column as the index of the data frame now. Plotting using Pandas is extremely easy.

df.plot()

We can also customize the plot easily.

df.plot(y=['dN',"dE","dU"],grid=True)
plt.ylabel("Amplitude")
plt.suptitle("GPS Data Visualization")
plt.title("0498")

If we want to save the figure, then we can use the command:

plt.savefig('0498Data.pdf',dpi=300,bbox_inches='tight')

This saves the figure as the pdf file named “0498Data.pdf”. The format can be set to any type “.png”, “.jpg”, ‘.eps”, etc. We set the resolution to be 300 dpi. This can be varied depending on our need. Lastly, “bbox_inches =‘tight’” crops our figure to remove all the unnecessary space.

Next Tutorial

We have loaded the data and visualized it. But we can see that our data has some trend and seasonality. In the future tutorial, we will learn how to remove that.

Python: a language for science

Python has become the most popular language for programming and its community is huge, active and ever-increasing. Before Python, MATLAB was the preferred language for the scientific community but now most of the researchers are migrating to Python. Like MATLAB, Python is quite easy to use but over that Python can be used for the system control, software developing, easy integration with other languages like FORTRAN, C , etc. This makes it extremely popular among all sorts of communities. Some P.Is want their students to work in Python because according to them, even when the students want to switch the field or simply leave the field, it could still be useful to them.

If you are familiar with other programming languages including MATLAB, then its very easy to switch to Python. Though, there are some issues the beginners and the MATLAB users face while making a move to Python. Here, let us deal with that issue and get started with Python.

Getting started with Python

Currently, there are two versions of Python – 2.7, and 3.6. But we will stick with Python 3.6. The steps for the version 2.7 is very similar.

Python can be downloaded directly from its official website https://www.python.org/downloads/.

But, here, we will download Python from the Anaconda website. Steps are listed below:

  1. Download the installer for the Windows, Mac, or the Linux system. For Windows, you will get a “.exe” extension file, double-click the file and follow the installation procedure.For Mac and Linux system, the file will be with the extension “.sh” (a shell- script). You can open your favorite terminal, navigate to the directory containing the downloaded Miniconda installation file. Then, you can simply type “sh Miniconda*.sh” and follow the steps prompted. You will be asked to accept the license and enter your installation location. If you don’t have any preferred location then the installer will install Miniconda in your home directory.

  2. Now, Miniconda, as well as Python 3.6, has been installed on your machine. We need some more Python libraries to get going. We can easily install these now using Miniconda. Open your terminal and type “conda install jupyter notebook pandas numpy matplotlib”.

We now have all the necessary libraries to get started with Python. Let us open a terminal again and simply type “jupyter notebook” to launch jupyter notebook. Jupyter notebook is a very popular interface which makes using Python a fun experience. It has all the features to make things simpler and useful. You can even run the shell command in the notebook. Over that, you can write your notes using the Markdown language, which is a very straight-forward language for writing. I strongly recommend you to learn Markdown. It won’t take more than 10 minutes to learn and will be useful in so many other places.

Now, that we have all the necessary tools to use Python then let’s use python to make a very simple plot.

  1. First, start jupyter notebook by typing “jupyter notebook” on your terminal.It will open “Jupyter” in your favorite browser.
  2. Now, go to the “New” tab at the top right corner and then select “Python 3”. It will open a new page for you.
  3. Let’s import some libraries which we have installed using the conda by typing the command as directed in the figure below. To execute the command, use the “Command/Ctrl + Enter” key.
  4. We also need to execute the command “%matplotlib inline” to keep our plots inline in the notebook. This is one of the many features of jupyter notebook.
  5. Let’s define our x and y values using the numpy library which we have imported as “np” for short-form.
  6. Let’s plot our data.

Writing NetCDF4 Data using Python

For how to read a netCDF data, please refer to the previous post. Also, check the package and tools required for writing the netCDF data, check the page for reading the netCDF data.

Importing relevant libraries

import netCDF4 
import numpy as np

Screen Shot 2017-10-03 at 2.20.50 PM.png

Let us create a new empty netCDF file named “new.nc” in the “../../data” directory and open it for writing.

ncfile = netCDF4.Dataset('../../data/new.nc',mode='w',format='NETCDF4_CLASSIC') 
print(ncfile)

Screen Shot 2017-10-03 at 2.30.59 PM.png

Notice here that we have set the mode to be “w”, which means write mode. We can also open the data in append mode (“a”). It is safe to check whether the netCDF file has closed, using the try and except statement.

Creating Dimensions

We can now fill the netCDF files opened with the dimensions, variables, and attributes. First of all, let’s create the dimension.

lat_dim = ncfile.createDimension('lat', 73) # latitude axis
lon_dim = ncfile.createDimension('lon', 144) # longitude axis
time_dim = ncfile.createDimension('time', None) # unlimited axis (can be appended to).
for dim in ncfile.dimensions.items():
 print(dim)

Screen Shot 2017-10-03 at 2.35.59 PM.png

Every dimension has a name and length. If we set the dimension length to be 0 or None, then it takes it as of unlimited size and can grow. Since we are following the netCDF classic format, only one dimension can be unlimited. To make more than one dimension to be unlimited follow the other format. Here, we will constrain to the classic format only as it is the simplest one.

Creating attributes

One of the nice features of netCDF data format is that we can also store the meta-data information along with the data. This information can be stored as attributes.

ncfile.title='My model data'
print(ncfile.title)

Screen Shot 2017-10-03 at 2.43.38 PM.png

ncfile.subtitle="My model data subtitle"
ncfile.anything="write anything"
print(ncfile.subtitle)
print(ncfile)
print(ncfile.anything)

Screen Shot 2017-10-03 at 2.45.55 PM.png

We can add as many attributes as we like.

Creating Variables

Now, let us add some variables to store some data in them. A variable has a name, a type, a shape and some data values. The shape of the variable can be stated using the tuple of the dimension names. The variable should also contain some attributes such as units to describe the data.

lat = ncfile.createVariable('lat', np.float32, ('lat',))
lat.units = 'degrees_north'
lat.long_name = 'latitude'
lon = ncfile.createVariable('lon', np.float32, ('lon',))
lon.units = 'degrees_east'
lon.long_name = 'longitude'
time = ncfile.createVariable('time', np.float64, ('time',))
time.units = 'hours since 1800-01-01'
time.long_name = 'time'
temp = ncfile.createVariable('temp',np.float64,('time','lat','lon')) # note: unlimited dimension is leftmost
temp.units = 'K' # degrees Kelvin
temp.standard_name = 'air_temperature' # this is a CF standard name
print(temp) 

Screen Shot 2017-10-03 at 2.51.29 PM.png

Here, we create the variable using the createVariable method. This method takes 3 arguments: a variable name (string type), data types, a tuple containing the dimension. We have also added some attributes such as for the variable lat, we added the attribute of units and long_name. Also, notice the units of the time variable.

We also have defined the 3-dimensional variable “temp” which is dependent on the other variables time, lat and lon.

In addition to the custom attributes, the netCDF provides some pre-defined attributes as well.

print("-- Some pre-defined attributes for variable temp:")
print("temp.dimensions:", temp.dimensions)
print("temp.shape:", temp.shape)
print("temp.dtype:", temp.dtype)
print("temp.ndim:", temp.ndim) 

Screen Shot 2017-10-03 at 2.57.36 PM

Since no data has been added, the length of the time dimension is 0.

Writing Data

nlats = len(lat_dim); nlons = len(lon_dim); ntimes = 3
lat[:] = -90. + (180./nlats)*np.arange(nlats) # south pole to north pole
lon[:] = (180./nlats)*np.arange(nlons) # Greenwich meridian eastward
data_arr = np.random.uniform(low=280,high=330,size=(ntimes,nlats,nlons))
temp[:,:,:] = data_arr # Appends data along unlimited dimension
print("-- Wrote data, temp.shape is now ", temp.shape)
print("-- Min/Max values:", temp[:,:,:].min(), temp[:,:,:].max())

Screen Shot 2017-10-03 at 3.02.52 PM.png

The length of the lat and lon variable will be equal to its dimension. Since the length of the time variable is unlimited and is subject to grow, we can give it any size. We can treat netCDF array as a numpy array and add data to it. The above statement writes all the data at once, but we can do it iteratively as well.

Now, let’s add another time slice.

data_slice = np.random.uniform(low=280,high=330,size=(nlats,nlons))
temp[3,:,:] = data_slice 
print("-- Wrote more data, temp.shape is now ", temp.shape) 

Screen Shot 2017-10-03 at 3.10.20 PM.png

Note, that we haven’t added any data to the time variable yet.

print(time)
times_arr = time[:]
print(type(times_arr),times_arr) 

Screen Shot 2017-10-03 at 3.12.50 PM.png

The dashes indicate that there is no data available. Also, notice the 4 dashes corresponding to the four levels in of the time stacks.

Now, let us write some data to the time variable using the datetime module of Python and the date2num function of netCDF4.

import datetime as dt
from netCDF4 import date2num,num2date
dates = [dt.datetime(2014,10,1,0),dt.datetime(2014,10,2,0),dt.datetime(2014,10,3,0),dt.datetime(2014,10,4,0)]
print(dates)

Screen Shot 2017-10-03 at 3.17.16 PM.png

times = date2num(dates, time.units)
print(times, time.units) # numeric values

Screen Shot 2017-10-03 at 3.18.53 PM.png

Now, it’s important to close the netCDF file which has been opened previously. This flushes buffers to make sure all the data gets written. It also releases the memory resources used by the netCDF file.

# first print the Dataset object to see what we've got
print(ncfile)
# close the Dataset.
ncfile.close(); print('Dataset is closed!')

Screen Shot 2017-10-03 at 3.23.38 PM.png

 

Earthquake Finder

This program can be used to obtain the earthquake information from various sources. The user can search for any event for given time range, magnitude range, depth range, geographical area. It can also obtain the focal mechanism solutions for the given parameters. It gives the output file (catalog.txt by default) where all the information is stored. It also plots the output (both with the focal mechanism and without it.)
This program makes use of the obspy module of Python and retrieve data from the International Seismological Center (ISC) server

Examples:

to run with default parameters

python3 earthquakeFinder.py

to obtain the earthquake info between today, March 2016 to the current time

python3 earthquakeFinder.py st=2016/3

to obtain the earthquake info between 2016, march, 29 to 2016, september, 22

python3 earthquakeFinder.py st=2016/3/29,et=2016/9/22

to obtain the catalog for magnitudes between 4-9 and with focal mechanism

python3 earthquakeFinder.py mxmag=9,mnmag=4,fm=yes

to obtain catalog for magnitude 4-7, and within radius of 10 (default) and central coordinates 22(lat),121(lon) with focal mechanism

python3 earthquakeFinder.py mxmag=7,mnmag=4,clat=22,clon=121,mxrad=80,fm=yes

focalmechanismcircularsearch

Parameters to change (default values in the braces):

mnla(-90),mxla(90),mnlo(-180),mxlo(180),mndep(0),mxdep(700),mnmag(4),mxmag(10),mnrad(0),mxrad(10),clat(None),clon(None),st(-1 month),et (current time),fm(no)

Output format of the catalog

Without Focal Mechanism -> “YEAR MONTH DAY HOUR MINUTES SECONDS LONGITUDE (in deg) LATITUDE(in deg) DEPTH(in km) MAG_TYPE MAG EVENT_NAME.”

With Focal Mechanism -> “YEAR MONTH DAY HOUR MIN SEC LONGITUDE LATITUDE DEPTH EXP(Nm) M0 MAG Mrr Mtt Mpp Mrt Mtp Mpr Str1 Dip1 Rake1 Str2 Dip2 Rake2.”

Requirements

  1. Python 3: Can be obtained from here.
  2. Extra Modules
    (a) requests: pip install requests
    (b) pandas: pip install pandas
    (c) obspy: pip install obspy
    (d) basemap: It is a great tool for creating maps using python in a simple way. The best way to obtain basemap is via Anaconda/MinicondaFor Linux/Mac users just download the bash installer and inside the download directory, execute the following command: bash Miniconda*.sh

    For Windows user, download the exe file and install it. After the installation of Anaconda/Miniconda, basemap can be obtained by simply executing the command conda install basemap


Click here
to download the programs.

 

Program for extracting the earthquake informations

Introduction

Often in seismology, we require the information about the earthquake such as location, origin time, depth, magnitude, etc. To obtain this information, users generally, browse the web or if he/she is experienced then just go to the predetermined sites such as global CMT catalog. Even, after reaching the correct website, we need to do some dig up to get the desired information. This program is meant to scrape the global CMT website to obtain the earthquake information.

How to obtain the program

You can download the package from here.

How to use the program

The package you download from the given site consists of two python programs. These programs require pre-installed python-3.

You can obtain python from the following websites:
1. Python software
2. The user can also download the python package anaconda

After installing the python 3, to run the program, type:
python3 EQinfo_extractor.py
Then enter the event recognition parameter such as
1976,3,8,4,39
And enter. It will prompt the event information.

Screen Shot 2017-08-27 at 10.07.05 PM

Using the program as a module

You can also use the package as a python module. For using it as a module, save the program in the current directory or in the computer-discoverable path.
import EQinfo_extractor as eq_ext
eq_ext.eventinfo(1976,3,8,4,39)