Plot a CTD profile

Here we import data from a .csv file containing data from a CTD profiler (depth, temperature, salinity and fluorescence).

1. First, download the CTD_profile.csv file, and put it in your working directory.

2. Import file…

# Extract data from file *********************************
import numpy as np

f = open('CTD_profile.csv', 'r')
data = np.genfromtxt(f, delimiter=',')
f.close()

3. Create variables

# Create variables with user-friendly names
depth = data[:,0]
temp  = data[:,1]
salt  = data[:,2]
fluo  = data[:,3]
del(data) # delete "data"... to keep things clean

4. Simple plot

# Plot data ***********************************************
import matplotlib.pyplot as plt
fig1 = plt.figure()
ax1 = fig1.add_subplot(111)
ax1.plot(temp,depth,'o-')

# Draw x label
ax1.set_xlabel('Temperature (C)')
ax1.xaxis.set_label_position('top') # this moves the label to the top
ax1.xaxis.set_ticks_position('top') # this moves the ticks to the top
#ax1.xaxis.tick_top() # ANOTHER way to move the ticks to the top

# Draw y label
ax1.set_ylabel('Depth (m)')
ax1.set_ylim(ax1.get_ylim()[::-1]) #this reverses the yaxis (i.e. deep at the bottom)

plt.show()

CTD_profile

5. More complex plot with subplots

# Three-panel plot
fig2, (ax2, ax3, ax4) = plt.subplots(1,3,sharey=True)
# Temperature
ax2.plot(temp,depth,'o-')
ax2.set_ylabel('Depth (m)')
ax2.set_ylim(ax2.get_ylim()[::-1]) #this reverses the yaxis (i.e. deep at the bottom)
ax2.set_xlabel('Temperature (C)')
ax2.xaxis.set_label_position('top') # this moves the label to the top
ax2.xaxis.set_ticks_position('top') # this moves the ticks to the top
# Salinity
ax3.plot(salt,depth,'o-r')
ax3.set_xlabel('Salinity')
ax3.xaxis.set_label_position('top') # this moves the label to the top
ax3.xaxis.set_ticks_position('top') # this moves the ticks to the top
ax3.yaxis.set_visible(False) # This erases the y ticks
# Fluorescence
ax4.plot(fluo,depth,'o-g')
ax4.set_xlabel('Flourescence (V)')
ax4.xaxis.set_label_position('top') # this moves the label to the top
ax4.xaxis.set_ticks_position('top') # this moves the ticks to the top
ax4.yaxis.set_visible(False) # This erases the y ticks

CTD_profile2

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3 thoughts on “Plot a CTD profile

  1. Pingback: T-S Diagram | Ocean Python

  2. To do the equivalent but straight from a .cnv (i.e. the SeaBird file itself), one can use the PyCNV package (http://cnv.castelao.net) instead of steps 1-3:

    pip install cnv
    from cnv import fCNV
    profile = fCNV(‘your_ctd_file.cnv’)

    # To check which variables are available
    profile.keys()

    # For example, here you can access the depth as:
    data[‘depth’]

    # And the temperature as:
    data[‘temperature’]

    # And to access the date of the profile from the CTD header:
    profile.attributes[‘datetime’]

  3. I am very new to programming and am trying to modify what you have for the CTD plots so that they all plot in one pane with multiple x-axes. Any idea how one would go about doing this? Thank you so much!

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