Using numpy/scipy with MsPASS


The numpy and scipy packages are heavily utilized for scientific computing in a wide range of fields. One of the reasons for that is performance. For a number of reasons that are beside the point, python arrays have horrible performance. That is particularly true of linear algebra operations common in all signal processing algorithms. All numpy algorithms we’ve ever tested are orders of magnitude faster than the same algorithm implemented as a pure python code with python arrays. Since most scipy algorithms are built on top of numpy, the same holds for scipy. Similarly, obspy uses numpy arrays exclusively. As a result, an early design constraint in MsPASS was to provide as clean an interface to numpy/scipy as possible. However, because we chose to implement our own core data objects in C++, that presents a disconnect that causes a few anomalies in the MsPASS API. This section of the User’s Manual documents these issues and provides guidance for how to effectively mix numpy/scipy algorithms with TimeSeries, Seismogram, and ensemble objects. It does not address a prototype data type we call a Gather that can be used for uniform ensembles. The Gather object is a pure python class that uses multidimensional numpy arrays to store sample data and is not subject to the issues addressed in this section.

TimeSeries Data

Recall the mspass TimeSeries class is used to abstract the concept of a single channel of fixed sample rate seismic data spanning a given time period. As such we used the standard signal processing abstraction of storing the data as a vector of numbers.

Every computing language that has any role in numerical computing defines a syntax for arrays. A vector in this context is a one-dimensional array. A problem with python’s builtin array is that it isn’t actually at all the same thing as an array in FORTRAN of C. Both FORTRAN and C define an array as a fixed block of memory of a specified length containing a sequence of numbers of the same type. (e.g. a C double array of length 10 is a block of \(8*10\) bytes.) Numpy performance is achieved by redefining an array to assume the data are in a contiguous memory block and using wrappers that allow low-level operations to actually be performed by compiled C or FORTRAN functions. We do the same thing in MsPASS but our data objects do not contain numpy array classes per se, but we use the same approach to allow low-level operations to be done in C++. Because we use the same concept (arrays are contiguous blocks of memory) the arrays can mostly be used interchangeably, but not always.

So what is the difference? If you execute this code fragment in MsPASS:

import numpy as np
from mspasspy.ccore.seismic import TimeSeries
x_numpy = np.zeros(100)
x_mspass = TimeSeries(100)
print("Type of numpy object=",type(x_numpy))
print("Type of mspass data vector=",type(

You should get this output:

Type of numpy object= <class 'numpy.ndarray'>
Type of mspass data vector= <class 'mspasspy.ccore.seismic.DoubleVector'>

The point is that both define two conceptually similar things that are a vector of sample data. In this example these are stored with the symbols x_numpy a The print statements emphasize they are different data types. They are not, however, an apples and oranges kind of comparison but more of a Jonathan versus Gala apple comparison. Python is very cavalier about type. Many sources call this “duck typing” from the cliche “if it walks like a duck and quacks like duck it must be duck”. Because of “duck typing” we can, in most cases, interchange the use of the two classes ndarray and DoubleVector. For example, you can nearly always send DoubleVector data to a numpy or scipy function and it will work just find. Here are a few examples:

import numpy as np
import scipy
# Setting data to nonzero values - not essential but otherwise
# trivial zero vector will cause problems for the log example
for i in range(x_mspass.npts):[i]=float(i+1)
x = np.log10(
y = np.sqrt(
yh = scipy.signal.hilbert(

That works because the DoubleVector is what numpy’s documentation calls “array like” (a duck type concept). In fact, any numpy or scipy function that accepts an “array like” argument can accept the data member of a TimeSeries and work. In reality, DoubleVector is a C++ “vector container” that in C++ would be declared as:

std::vector<double> x;

In MsPASS we use stock “bindings” from pybind11 that allow us to do this magic. The real magic is that in most cases no copying of the array data is required. (For C programmers the bindings use a pointer (address) not a copy.)

This magic works for most, but not necessarily all, vector operators that mix DoubleVector and ndarray types. e.g. with the symbols above defined all of the following will work and do what is expected: -= z
z=x_numpy*  # a peculiar numpy operation - not a dot product *= 10.0

The main thing to avoid is an assignment where the left hand side and right hand side resolve to different types. For instance, the following will fail with a TypeError exception if you try to run it:

z=np.ones(100) = x_numpy = x_numpy + z

The solution is to use a python version of a type cast to a DoubleVector: = DoubleVector(x_numpy) = DoubleVector(x_numpy + z)

That is necessary because in both cases the right hand side is an ndarray. The construct used is a call to the bindings of a copy constructor for the C++ std::vector container so it seems to come at the cost of a memory copy. On the other hand, that is orders of magnitude faster than a python loop to do the same operations.

Be aware that if you mix types in a vector operation you can get some surprising results. For example, the following code will generate a TypeError exception:

z=np.ones(100) = z +

while simply reversing the order of z and like this

z=np.ones(100) = + z

works and does set to the vector sum of the two symbols on the right hand side. The reason is that the + operator in python seems to resolve the type to the type of the left side of the + operator. Why is “deep in the weeds”, but the best advice is to avoid mixed type operations if possible. The more robust way to write the above as:

z = np.ones(100)
x = z + np.array( = DoubleVector(x)

Finally, users who are matlab fans may like to write python code using the vector “:” operator. For example, with numpy functions operations like the following are commonly used:


That will print “5” - the length of the subvector extracted in x. The : operator does not always work with a DoubleVector. If you have an algorithm using the colon operator, do the vector operations with numpy and then copy the result into the TimeSeries data member. An important warning about any such assignments to is you MUST be sure the size of the vector on the right hand side is the same size as the left hand side. Consider this segment:  # creates data vector 100 samples long
x=z[5:10] = DoubleVector(x)

The output of this is “5” showing that, as expected, is replaced by the subvector x. The BIG PROBLEM that can cause is it will create an inconsistency in the size set by the npts attribute of TimeSeries. The correct solution for the above is this minor variant calling the set_npts method of TimeSeries  # creates data vector 100 samples long
ts.set_npts(5) = DoubleVector(x)

Seismogram Data

MsPASS uses a different data type to hold data from three-component sensors. The motivation is described in the section titled Data Object Design Concepts. The result is that the array holding the sample data is a matrix instead of a vector. Some implementation details of note are:

  1. In MsPASS the matrix has 3 rows and npts columns. That means the rows of the matrix an be extracted to create a TimeSeries subset of the data while the columns are single “vector” samples of ground motion.

  2. Currently MsPASS uses a simple, lightweight matrix class to store the sample data called mspasspy.ccore.utility.dmatrix. A key reason we made that choice was control over methods defined for the class. A case in point is the shape attribute that we will see momentarily is important for working with numpy.

  3. For performance dmatrix is implemented in C++. The class has methods for all standard matrix operations with python bindings for those operator. The corollary to that statement is that when working with Seismogram data use the native operators when possible.

  4. A dmatrix stores the array data in a contiguous block of memory in what numpy would call “FORTRAN order”. (“C order” is reversed.) FORTRAN stores a matrix as a contiguous block of memory with the row index “varying fastest”. Exchanging the sample data stored this way with numpy is like that with the std::vector used in TimeSeries but the exchange uses a pointer to the first sample of the contiguous block of memory held by an instance of a dmatrix class referenced with the symbol

  5. We use a variation of the same “magic” in the pybind11 binding code that allows the matrix to interact cleanly with numpy and scipy functions that require a matrix. Like the scalar case there are impedance mismatches, however, that can complicate that exchange. We discuss these below.

Almost all of what was discussed above about using TimeSeries arrays with numpy are similar. For example, although the result is meaningless, you can run the following code snippet with MsPASS and it will run and produce the expected result:

import numpy as np
from mspasspy.ccore.seismic import Seismogram
x_mspass =Seismogram(100)
# initialize the matrix to some meaningless, nonzero values
for i in range(3):
  for j in range(x_mspass.npts):[i,j]=i+j+1
# these apply the math operation for each number in the data matrix
# matrix operation that multiplies all samples by 2.0 *= 2.0
# matrix operator adding content of numpy matrix z to data matrix + z
# matrix operation adding y and matrices += y
# Same thing done with a binary + operator
# use a copy to show more likely use
x_mspass_data = z + y

As with TimeSeries at mismatch will occur if the operation yields a type mismatch. For example, the following minor variant of above will run:

y=np.ones([3,100]) = + y

In contrast, the following that might seem completely equivalent will raise a TypeError exception:

y=np.ones([3,100]) = y +

The reason is that for the right hand side resolves to a numpy “ndarray” and the left hand side is a dmatrix. Exactly like above, this simpler assignment will fail exactly the same way: = y

The solution is similar to that we used above for TimeSeries: = dmatrix(y)

That is, DoubleVector is changed to dmatrix.

Finally, the warnings above about the “:” operator with TimeSeries apply equally to Seismogram. If you write a python code with the color operator do all those operations with numpy arrays and use the dmatrix copy constructor to load the result into the object’s data array. The warning about making sure the npts member attribute is consistent with the result applies as well. The only thing to remember with a Seismogram is that npts is the number of columns of the data matrix, not the total number of samples.