Notebook

PySeison - Tutorial 1: FVCOM class¶

In [1]:

%pylab inline

Populating the interactive namespace from numpy and matplotlib

1. PySeidon - FVCOM object initialisation¶

Similarly to the "Station class", the "FVCOM class" is a numerical-model-based object.

1.1. Package importation¶

As any other library in Python, PySeidon has to be first imported before to be used. Here we will use an alternative import statement compared to the one previoulsy presented:

In [2]:

from pyseidon import *

*** Star *** here means all. Usually this form of statements would import the entire library. In the case of PySeidon, this statement will import the following object classes: FVCOM, Station, Validation, ADCP, Tidegauge and Drifter. Only the FVCOM class will be tackle in this tutorial. However note should note that the architecture design and functioning between each classes are very similar.

1.2. Object definition¶

Python is by definition an object oriented language...and so is matlab. PySeidon is based on this notion of object, so let us define our first "FVCOM" object.

*Exercise 1: *

Unravel FVCOM documentation with Ipython *shortcuts*

*Answer: *

In [3]:

FVCOM?

According to the documentation, in order to define a FVCOM object, the only required input is a *filename. This string input represents path to a file (e.g. testFvcom=FVCOM('./path_to_FVOM_output_file/filename') and whose file can be a pickle file (i.e. .p) or a netcdf file (i.e. .nc). Additionally, either a local file path or a OpenDap url could be used.

Optionally, one can extract spatial and/or temporal data from the designated file by respectively defining *ax* and *tx keywords. *ax* can be defined as a list of min/max longitudes and latitudes (e.g. ax = [minimum longitude, maximum longitude, minimum latitude, maximum latitude]) or as a pre-defined region tag (e.g. ax = 'GP', 'PP', 'DG' or 'MP'). Whereas *tx* can be defined as a list of date (e.g. tx = ['2012-11-07T12:00:00','2012.11.09T12:00:00']).

One should note that throughout the package, the following conventions apply:

Date = string of 'yyyy-mm-ddThh:mm:ss'
Coordinates = decimal degrees East and North
Directions = in degrees, between -180 and 180 deg., i.e. 0=East, 90=North, +/-180=West, -90=South
Depth = 0m is the free surface and depth is negative

*Exercise 2: *

define a FVCOM object named fvcomOD from an opendap url
define a FVCOM object named fvcomPartial1 from the same opendap url using ax and tx keywords
define a FVCOM object named fvcomPartial2 from the same opendap url using the same ax but a consecutive tx period

*Answer: *

In [4]:

fvcomOD=FVCOM('http://ecoii.acadiau.ca/thredds/dodsC/ecoii/test/FVCOM3D_dngrid_BF_20130619_20130621.nc')

Retrieving data through OpenDap server...
Initialisation...

In [5]:

ax=[-65.77, -65.75, 44.675, 44.685]
tx1=['2013-06-20 12:00:00', '2013-06-21 12:00:00']
tx2=['2013-06-21 12:00:00', '2013-06-21 18:00:00']
fvcomPartial1=FVCOM('http://ecoii.acadiau.ca/thredds/dodsC/ecoii/test/FVCOM3D_dngrid_BF_20130619_20130621.nc', ax=ax, tx=tx1)
fvcomPartial2=FVCOM('http://ecoii.acadiau.ca/thredds/dodsC/ecoii/test/FVCOM3D_dngrid_BF_20130619_20130621.nc', ax=ax, tx=tx2)

Retrieving data through OpenDap server...
Initialisation...
Re-indexing may take some time...
-Now working in bounding box-
-Now working in time box-
Retrieving data through OpenDap server...
Initialisation...
Re-indexing may take some time...
-Now working in bounding box-
-Now working in time box-

1.3. Object attributes, functions, methods & special methods¶

The FVCOM object possesses 4 attributes, 4 methods (or 3 for 2D simulations) and 1 special method. They would appear by typing *fvcomOD. Tab* for instance.

An attribute is a quantity intrinsic to its object. A method is an intrinsic function which changes an attribute of its object. Contrarily a function will generate its own output:

object.method(inputs) output = object.function(inputs)

The FVCOM attributes are:

*History*: history metadata that keeps track of the object changes
*Data: gathers the raw/unchanged data of the specified .nc file
*Grid*: gathers the grid related data
*Variables*: gathers the hydrodynamics related data. Note that methods will generate new fields in this attribute

The FVCOM methods & functions are:

*Util2D*: gathers utility methods and functions for use with 2D and 3D variables
*Util3D*: gathers utility methods and functions for use only with 3D variables. Note that this attribut will not appear for 2D simulations.
*Plots*: gathers plotting methods for use with 2D and 3D variables
*Save_as*: save loally the current object and its attributs in a pickle file or a matlab file. Note that the so created pickle file can be use later on to define a FVCOM object and therefore restart your work where you left it...yet be careful what you wish for!!! Be aware that FVCOM runs can be very large in terms of memory when you decide to save anything from OpenDap.

The special FVCOM method permits to *stack* two FVCOM objects (e.g. fvcom1 and fvcom2) through a simple addition, as such:

fvcom1 += fvcom2

However, fvcom1 and fvcom2 must share the exact same spatial domain and be consecutive in time (e.g. fvcom1 before in time compared to fvcom2).

*Exercise 3: *

check fvcomPartial1's History attribute
*stack* fvcomPartial2 to fvcomPartial1
check fvcomPartial1's History attribute
*save* fvcomPartial1 on your machine

*Answer: *

In [6]:

fvcomPartial1.History

Out[6]:

['Created from http://ecoii.acadiau.ca/thredds/dodsC/ecoii/test/FVCOM3D_dngrid_BF_20130619_20130621.nc',
 'Bounding box =[-65.77, -65.75, 44.675, 44.685]',
 'Temporal domain from 2013-06-20 12:00:00 to 2013-06-21 12:00:00']

In [7]:

fvcomPartial1 += fvcomPartial2

In [8]:

fvcomPartial1.History

Out[8]:

['Created from http://ecoii.acadiau.ca/thredds/dodsC/ecoii/test/FVCOM3D_dngrid_BF_20130619_20130621.nc',
 'Bounding box =[-65.77, -65.75, 44.675, 44.685]',
 'Temporal domain from 2013-06-20 12:00:00 to 2013-06-21 12:00:00',
 'Data from FVCOM3D_dngrid_BF_20130619_20130621.nc has been stacked']

Note how the *History* attribute has changed

2. PySeidon - Hands-on (30 mins)¶

*Exercise 4: *

Plot *colormap* of fvcomPartial1's bathymetry
Plot *colormap* of fvcomOD's bathymetry

*Answer: *

In [14]:

fvcomPartial1.Plots.colormap_var(fvcomPartial1.Grid.h, title='Bathymetry (m)', mesh=False)

In [16]:

fvcomOD.Plots.colormap_var(fvcomOD.Grid.h, title='Bathymetry (m)', isoline='none')

*Exercise 5: *

compute the 3D *velocity norm* for the entire fvcomPartial1
compute the time indices *ebb* and *flood* for refPoint=[-65.761, 44.68]
use *np.mean* to compute the time-averaged 3D velocity norm for *ebb* indices, ebbNorm
use *np.mean* to compute the time-averaged 3D velocity norm for *flood* indices, floodNorm
plot a *vertical slice of ebbNorm* between pointD=[-65.76246, 44.67976] and pointB=[-65.76053, 44.68023]
plot a *vertical slice of floodNorm* between pointA=[-65.76178, 44.68057] and pointC=[-65.76123, 44.67942]
check fvcomPartial1's *History* attribute

*Answer: *

In [11]:

refPoint=[-65.761, 44.68]
pointA=[-65.76178, 44.68057]
pointB=[-65.76053, 44.68023]
pointC=[-65.76123, 44.67942]
pointD=[-65.76246, 44.67976]

fI, eI, pa, pav= fvcomPartial1.Util2D.ebb_flood_split_at_point(refPoint[0], refPoint[1])
fvcomPartial1.Util3D.velo_norm()
ebbNorm = np.mean(fvcomPartial1.Variables.velo_norm[eI,:,:], 0)
floodNorm = np.mean(fvcomPartial1.Variables.velo_norm[fI,:,:], 0)
fvcomPartial1.Plots.vertical_slice(ebbNorm, pointD, pointB, title='Time-averaged velocity norm (m/s)')
fvcomPartial1.Plots.vertical_slice(floodNorm, pointA, pointC, title='Time-averaged velocity norm (m/s)')
fvcomPartial1.History

-Velocity norm added to FVCOM.Variables.-

Out[11]:

['Created from http://ecoii.acadiau.ca/thredds/dodsC/ecoii/test/FVCOM3D_dngrid_BF_20130619_20130621.nc',
 'Bounding box =[-65.77, -65.75, 44.675, 44.685]',
 'Temporal domain from 2013-06-20 12:00:00 to 2013-06-21 12:00:00',
 'Data from FVCOM3D_dngrid_BF_20130619_20130621.nc has been stacked',
 'Velocity norm computed']

*Exercise 6: *

Using fvcomOD
Plot the vertical shear profile averaged over ebb indices for a point of your own choice
Plot rose diagram and exceedance curve for the same point with flow dir at point
Plot flow velocity histogram for the same point with speed_histogram
Plot a colormap of the bathymetry, add a point at the location of your point

*Answer: *

In [12]:

point = [-66.0, 45.0] #refPoint
fI, eI, pa, pav= fvcomOD.Util2D.ebb_flood_split_at_point(point[0], point[1])
vp = fvcomOD.Util3D.verti_shear_at_point(point[0], point[1], time_ind=eI, graph=True)
fD, norm = fvcomOD.Util2D.flow_dir_at_point(point[0], point[1], exceedance=True)
fvcomOD.Util2D.speed_histogram(point[0], point[1])
fvcomOD.Plots.colormap_var(fvcomOD.Grid.h, title='Bathmetry (m)', mesh=False)
fvcomOD.Plots.add_points(point[0], point[1], label='Location')

3. PySeidon - to infinity and beyond (30 mins)¶

PySeidon can easily be coupled to any other Python library and package. For instance, the following script creates a series of *.png which could be then easily turn into an animated GIF with GIMP:

In [ ]:

fvcomPartial1.Util2D.hori_velo_norm()
import matplotlib.pyplot as plt
for i in range(fvcomPartial1.Grid.ntime):
    fvcomPartial1.Plots.colormap_var(fvcomPartial1.Variables.hori_velo_norm[i,:], title='Flow speed (m/s)')
    saveName = 'anim{0}.png'.format(i)
    plt.savefig(saveName, bbox_inches=0)
    plt.close()

4. PySeidon - Bug patrol & steering committee¶

4.1. Bug report¶

As beta tester, your first assignement is to report bugs...yet not everything is a bug. The first thing to check before to report a bug is to verify that your version of PySeidon is up-to-date. The best way to keep up with the package evolution is to *git* to *clone* the repository, use *pull* to update it and *re-install* it if needed.

The second thing to check before to report a bug is to verify that the bug is *reproducible. When running into a bug, double check that your inputs fit the description of the documentation then turn the debug flag on* (e.g. output = fvcomobject.function(inputs, debug=True)) and submit the command again. If the error re-occurs then report it (i.e. copy entire error message + command and send it to package administrator)

4.2. Suggestions & critics¶

Your second role as beta-tester is to submit suggestions and critics to the developpers regarding the functioning and functionality of the package. Beta testing phase is the best opportunity to steer a project towards the applications you would like to be tackled...