I would like to be able to save the TEXT output of an iPython notebook cell into a file on disk.
I have 2 additional requirements/requests:
be able to re-run the cell and overwrite my output with whatever the latest is.
also display the output within the notebook.
I have figured out how to use the %%capture magic for some basic saving of an iPython notebook's cell into a file, but it does not seem flexible enough: it keeps appending every time I re-run the cell and I cannot get it to display within the same cell.
Here is what I have so far:
%%capture cap --no-stderr
print 'stuff'
with open('output.txt', 'w') as f:
f.write(cap.stdout)
# clear the cap by deleting the variable here?
# del cap
When I try to put cap.show() after the write, it does not seem to display. Instead, it puts the output into the cap variable twice.
You have a typo, missing d in cap.stout. It should be cap.stdout
I tested the following and it worked fine. cap.show() also printed "stuff" and re-running the cell overwrote the file.
%%capture cap --no-stderr
print 'stuff'
with open('output.txt', 'w') as f:
f.write(cap.stdout)
%%capture cap --no-stderr
print("a")
with open('output.txt', 'w') as f:
f.write(str(cap))
Related
I want to suppress any text output when I run Jupyter Notebook cell. Specifically I output some figures and each is accompanied by something like:
<Figure size 432x288 with 0 Axes>
I have seen that if I put a ; at the end of a line, it should suppress the output, but it is not working in my case.
The code:
for i in tqdm_notebook(range(data.shape[0])):
print('BIN:',i)
fig = plt.figure(figsize=(15,4))
plt.tight_layout()
gs = gridspec.GridSpec(2,1)
ax1 = fig.add_subplot(gs[0, 0])
ax1.plot(match[window_begin:window_end],'k')
plt.vlines(i,-np.max(match[window_begin:window_end])*0.05,np.max(match[window_begin:window_end])*1.05,'r',linewidth=4,alpha=0.2)
ax1.set_xlim(0-1,post_bin_match_median[window_begin:window_end].shape[0])
ax1.set_ylim(-np.max(match[window_begin:window_end])*0.05,np.max(match[window_begin:window_end])*1.05)
plt.tick_params(axis='y', which='both', left=True, labelleft=False)
ax1.tick_params(axis='x', which='both', bottom=False, labelbottom=False)
plt.grid()
ax2 = fig.add_subplot(gs[1, 0])
fig.subplots_adjust(hspace=0.0)
ax2.plot(gp_mjds[:],gp_data[i,:],'k')
ax2.errorbar(remain, all[i,:], yerr=all_noise[i], fmt=".k", capsize=0);
ax2.fill_between(gp[:], gp2[i,:] - np.sqrt(gp_var[i,:]), gp2[i,:] + np.sqrt(gp_var[i,:]),color="k", alpha=0.2)
ax2.set_xlim(gp[0],gp[-1])
plot_y_min = np.minimum(np.min(gp2[:,:] - np.sqrt(gp_var[:,:])),np.min(all_profile_residuals[:,:]-y_noise))
plot_y_max = np.maximum(np.max(gp2[:,:] + np.sqrt(gp_var[:,:])), np.max(all[:,:]+y_noise))
ax2.set_ylim(plot_y_min,plot_y_max)
plt.grid()
plt.show()
plt.clf()
plt.close(fig);
The semi-colon would work if the typical output from the last line of the cell is what you are trying to suppress. As succinctly summarized by #kynan here, "The reason this works is because the notebook shows the return value of the last command. By adding ; the last command is "nothing" so there is no return value to show."
However, you have a loop inside a cell generating objects.
The culprit seems to be plt.clf(). Comment out that line or remove it from your code, and it should fix it.
Plus, I'd remove plt.show() as it isn't necessary when plt.clf() is removed, and I am seeing it being in the loop causing fig = plt.figure(figsize=(15,4)) to also show output text like you posted in your issue.
(I'll add for others looking at this later, that it is important have %matplotlib inline or %matplotlib notebook at the start of the cell (or at the start of a cell somewhere above this one.))
A complete guide on how to hide or remove content in Jupyter is available from the official documentation: https://jupyterbook.org/interactive/hiding.html#
For removing the single output line, you can tweak the command lines by adding a _ = [command ] assignment as suggested in this blog: https://www.tutorialguruji.com/python/suppress-output-in-matplotlib/.
The underscore there is a throwaway variable, actually an unidentified variable "when not in interactive mode". See the official Python documentation: https://docs.python.org/3.9/reference/lexical_analysis.html#reserved-classes-of-identifiers
So, I am essentially just dreaming up ideas right now.
I was wondering if it was possible to make a python program that can read a document, take a line from the document, make an if/else statement with it (Like if the text on that line is equal to Hello, than say hello back), and then continue onto the next line. I have already kind of done this in a shell fashion but I want to see if it is possible to have python read the line of a document, interpret it, display something, and move on to the next line of the document.
(I am prepared for this post to get tons of -1's for not knowing how to program a lot of python, and probably just not being clear enough. So before you -1, just add a comment saying what you need me to be clear about.)
The version of python of my choice would be 2.5.
Since you don't know any Python, try this:
with open("file.txt") as f:
for line in f:
if line.strip() == "Hello":
print "Hello back"
or without the exception-safe clause:
for line in open("file.txt"):
if line.strip() == "Hello":
print "Hello back"
the strip() removes the ending newline \n from the line
That is actually a very simple task in Python:
file = open("file.txt") # open the file
while True:
word = file.readline() # read a line from the file
print word # print it to the console
if word == "": # if out of words...
file.close() # ...close the file
break # and break from while loop and exit program
I'm making a small program to trace the execution flow of a program. I have some files that have source code and some that don't. For calls that happen in files without source, I'm trying to count them and tack that number to the end of the output line.
From what I understand I'm positioning the cursor 3 characters from the end and then when I write output to myfile, it should have overwritten the previous 3 characters. But when I look in the file, those 3 characters are just getting appended to the end.
with open("C:\\Windows\\Temp\\trace.html", "a+") as myfile:
if hasNoSource and not fileHasChanged:
myfile.seek(-3,2)
output = line
else:
self.noSourceCallCount = 0
myfile.write(output)
return self.lineHook
"a+" mode is open for append mode and any changes by seek() will be reset by next write(). Use "r+" mode.
fileinput module with the inplace option allows you to modify your file but be sure to make a backup if all hell break loose
import fileinput,sys,re
line_count=0
for line in open(my_file):
line_count+=1 # count total lines in file
f=fileinput.input(my_file,inplace=True)
for line in f:
line_count-=1 #when iterating through every line decrement line_count by 1
if line_count==0:
line=re.sub("...$",<replacement>,line) #use regex to replace first three characters in the last line
sys.stdout.write(line) #print line to sys.stdout which will automatically make the changes to this line in file.
else:
sys.stdout.write(line)
Sometimes my Ipython notebooks crash because I left a print statement in a big loop or in a recursive function. The kernel shows busy and the stop button is usually unresponsive. Eventually Chrome asks me if I want to kill the page or wait.
Is there a way to limit the number of output lines in a given cell? Or any other way to avoid this problem?
You can suppress output using this command:
‘;’ at the end of a line
Perhaps create a condition in your loop to suppress output past a certain threshold.
For anyone else stumbling across:
If you want to see some of the output rather than suppress the output entirely, there is an extension called limit-output.
You'll have to follow the installation instructions for the extensions at the first link. Then I ran the following code to update the maximum number of characters output by each cell:
from notebook.services.config import ConfigManager
cm = ConfigManager().update('notebook', {'limit_output': 10})
Note: you'll need to run the block of code, then restart your notebook server entirely (not just the kernel) for the change to take effect.
Results on jupyter v4.0.6 running a Python 2.7.12 kernel
for i in range(0,100):
print i
0
1
2
3
4
limit_output extension: Maximum message size exceeded
I'm using Atom with soft wrap turned on. In most simple editors such as gedit, Ctrl-Down would be used to skip ahead to the true next line, ignoring any wrapped lines below (same as j and k in Vim).
However in Atom this shortcut produces the result of moving the line itself around, which is less useful to me. I'd like to remap Ctrl-Up and Ctrl-Down to move the cursor up or down to the next true line, as described above.
I'm familiar with editing my keymap file, but I simply can't find any command that would be the equivalent of moving ahead one full line.
You could write a custom command in your init.coffee like this:
atom.workspaceView.command 'custom:move-next-buffer-line', ->
editor = atom.workspace.getActiveEditor()
editor.moveCursorToEndOfLine()
editor.moveCursorRight()
And then just reverse it for moving to the previous buffer line. You can then map the custom command in your keymap, which you said you're familiar with.
If you're using the vim-mode-plus package, then just modify your keymap.cson file by adding
# except insert
# -------------------------
'atom-text-editor.vim-mode-plus:not(.insert-mode)':
# Motions
# -------------------------
'k': 'vim-mode-plus:move-up-screen'
'j': 'vim-mode-plus:move-down-screen'
See for details https://github.com/t9md/atom-vim-mode-plus/blob/master/keymaps/vim-mode-plus.cson