I want to run a python recipe I found, but I don't know how as it imports from another one!
For example, I would like to test the code here.
I have downloaded it and also downloaded this one as it uses it.
So how can I test the this code by passing the needed parameter as below?!
>>> G = {'s':{'u':10, 'x':5}, 'u':{'v':1, 'x':2}, 'v':{'y':4}, 'x':{'u':3, 'v':9, 'y':2}, 'y':{'s':7, 'v':6}}
>>> Dijkstra.Dijkstra(G,'s','v')
I have added the two files in one of the python paths, and imported both but still get error
Could you please give me some advice on simple way to test this code?
You really should put the files in your current directory if you are just testing, instead of putting them in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ as that path is reserved for the Python standard library.
It seems that the second recipe, the Priority Dictionary, needs to be put in a file called priodict.py since the Dijkstra code imports from priodict. So, you should have the following files in your current directory: Dijkstra.py, priodict.py. Then you can just start Python and do import Dijkstra, and it should work.
Also, don't modify the Dijkstra code to remove the import as you apparently did...
Related
I have been playing with Tkinter in Python 2.7, and just ran across something that SHOULD be a bug, but isn't and the program seems to work OK still.
To make my program more manageable, I have split it into separate .py files.
One file (called globs.py) is a list of global variables in the form
global var_1
global var_2
...
Then I import globs into my other files.
In another file I can set the variable, thus...
import globs
globs.var_1 = "some value"
In a third file I can use it..
import globs
if globs.var_1 == "something":
...
So far, all is as expected, but...
I just found out if the variable is NOT mentioned in the globs.py file at all, the program still seems to work OK.
Is this intended behavior? Any other programming language would give a 'variable not found' error.
If it is intended, why should I even setup any variables in globs.py?
What are the drawbacks?
Thanks, Mark.
I'm using Knime 3.1.2 on OSX and Linux for OPENMS analysis (Mass Spectrometry).
Currently, it uses static filename.mzML files manually put in a directory. It usually has more than one file pressed in at a time ('Input FileS' module not 'Input File' module) using a ZipLoopStart.
I want these files to be downloaded dynamically and then pressed into the workflow...but I'm not sure the best way to do that.
Currently, I have a Python script that downloads .gz files (from AWS S3) and then unzips them. I already have variations that can unzip the files into memory using StringIO (and maybe pass them into the workflow from there as data??).
It can also download them to a directory...which maybe can them be used as the source? But I don't know how to tell the ZipLoop to wait and check the directory after the python script is run.
I also could have the python script run as a separate entity (outside of knime) and then, once the directory is populated, call knime...HOWEVER there will always be a different number of files (maybe 1, maybe three)...and I don't know how to make the 'Input Files' knime node to handle an unknown number of input files.
I hope this makes sense.
Thanks!
Thanks to Gábor for getting me on the right track. Although I ended up doing a slightly different route after much experimentation.
===
Being new to Knime, I don't know if this is an efficient use of Knime, or a complete Kluge...but it does work.
So, part of the problem is some of the Knime specific objects - One of which is called URIDataValue.
A Python Pandas dataframe is, apparently, interchangable with the Knime tables. However, I don't know if there's a way to import one of these URIDataValue objects into Python. So here's what I did...
1. I wrote a Python script that creates a Pandas Dataframe, and populates it with one Column. Everything is a string, including the column header:
from pandas import DataFrame
# Create empty table
T = DataFrame(
[
['file:///Users/.../copy/lfq_spikein_dilution_1.mzML'],
['file:///Users/.../copy/lfq_spikein_dilution_2.mzML'],
],
)
T.columns = ['URIDataValue']
#print T
output_table = T
That creates this dataframe:
Note: The column name and values are just strings. But it is (apparently) important that the column header be 'URIDataValue'...even though HERE it's just text. If the column name is not 'URIDataValue' the next node doesn't know what to do.
NEXT, the 'output_table' from the 'Python Source' node is patched to a 'String to URI' node, which (apparently and magically) knows to change the entire columns string values to URIDataValues (presumably based on the name of the first column...don't know that for sure).
Finally, the NEW table, with the correct data objects goes to a 'URI to PORT' node...since apparently 'Port' objects and a 'URI' object are different.
This, then, matches the needed input to the ZipLoop...which is normally the out put from a static (hard coded) 'Input Files' node.
Now, to actually solve the question above, I just have to add the code to my 'Python Source' to download and unzip the S3 files, then annotate the dataframe with their locations, and go.
I have no idea what I'm doing, but it worked.
There are multiple options to let things work:
Convert the files in-memory to a Binary Object cells using Python, later you can use that in KNIME. (This one, I am not sure is supported, but as I remember it was demoed in one of the last KNIME gatherings.)
Save the files to a temporary folder (Create Temp Dir) using Python and connect the Pyhon node using a flow variable connection to a file reader node in KNIME (which should work in a loop: List Files, check the Iterate List of Files metanode).
Maybe there is already S3 Remote File Handling support in KNIME, so you can do the downloading, unzipping within KNIME. (Not that I know of, but it would be nice.)
I would go with option 2, but I am not so familiar with Python, so for you, probably option 1 is the best. (In case option 3 is supported, that is the best in my opinion.)
I'm using Enthought Canopy with PyLab(64-bit). For my report I need to use Latex (XeLaTex) and the plots are done with matplotlib.
To have an first idea I just copied the second example from http://matplotlib.org/users/usetex.html and compiled it. It looks fine and I can save it as a normal png without problems. However if i try to save it as .eps or.ps it does not work and an error appears:
invalid literal for int() with base 10: "
Additionaly in the Pylab shell it shows:
'gswin32c' is not recognized as an internal or external command, operable program or batch file'.
If I save it as .pdf I have no problems except the text is all black instead of being red and blue. This is a problem because in my plots I have two axes and I need them colorized for better readability.
If I then try to delete some lines from the example given (all text) I still cannot save it as .eps nor .ps. I can't figure out the problem and all the other topics related to this have not given me an insight. So I really need your help because I can't use .png for my report.
Thank you in advance!!!
I finally managed to solve this problem. It might look weird but maybe other people can benefit from it.
The solution might depend upon the software you use. I use Enthought Canopy (Python) and MikTeX 2.9 under W8 64bit.
If you want to output .ps and .eps files with matplotlib using the 'text.usetex': True option then you will encounter the problem posted above.
Solution:
Download and install Ghostscript (32bit) from http://www.ghostscript.com/download/gsdnld.html.
Download ps2eps-1.68.zip from http://www.tm.uka.de/~bless/ps2eps. The proceeding is given in the manual, however I like to point out the part with the environment variables. In this last step you need to go to Control Panel --> System --> Advanced system settings. Then click on the header 'Advanced' and on the bottom of the window you see 'Environment Variables' on which you click. Then you use the 'New'-Button for User Variables for USERNAME. Then you type in as variable name 'ps2eps' and for variable value you type in the actual path where you have saved the ps2eps.pl file. In my case this is 'C:\Program Files (x86)\ps2eps\bin\'. You can check if you type 'ps2eps' in the command-window.
Download xpdfbin-win-3.03.zip from http://www.foolabs.com/xpdf/download.html. You only need the file 'pdftops.exe'. However I could not assign a path like in step 2. I solved this by putting the 'pdftops.exe' in the MikTeX 2.9 folder. The exact location for me was 'C:\Program Files\MiKTeX 2.9\miktex\bin\x64'.
I was then able to save figures as .ps and have no more any error messages. Remember to use the settings proposed on http://matplotlib.org/users/usetex.html under 'postscript options'.
In myself used the following settings:
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import matplotlib as mpl
mpl.rc('font', **{'family':'serif', 'serif':['Computer Modern Roman'],
'monospace':['Computer Modern Typewriter']})
params = {'backend': 'ps',
'text.latex.preamble': [r"\usepackage{upgreek}",
r"\usepackage{siunitx}",
r"\usepackage{amsmath}",
r"\usepackage{amstext}",],
'axes.labelsize': 18,
#'axes.linewidth': 1,
#'text.fontsize':17,
'legend.fontsize': 10,
'xtick.labelsize': 13,
#'xtick.major.width' : 0.75,
'ytick.labelsize': 13,
'figure.figsize': [8.8,6.8],
#'figure.dpi': 120,
'text.usetex': True,
'axes.unicode_minus': True,
'ps.usedistiller' : 'xpdf'}
mpl.rcParams.update(params)
mpl.rcParams.update({'figure.autolayout':True})
(whereas many of the params are just for my own purpose later in the plots)
As a beginner I am not well informed about the dependence from the 'backend' used if you are running a script from your python console. I however used this without any --pylab settings in before and I do not know if one needs to switch the backend manually if he is working already in a console with a specific matplotlib backend.
I had the same problem and my problem was a font adjustment in the python code that is :
from matplotlib import rc
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
rc('text', usetex=True)
when I remove this iit works fine and now i can save eps.
So be sure that any shortest working example is working for you or not then check the font and other style edits in your code. This may help.
first post to SO, so if I'm missing some details, please forgive me.
Is there a way to use relative paths from another subfolder without resorting to modifying sys.path via os? Eventually this will be run from a cgi webserver so I'd rather stay away from any -m arguments to python.exe.
I'm using Python 2.7.3 and have a file/directory structure of the following :
| myprog.py
|
+---functions
| myfunctions.py
| __init__.py
|
\---subfolder
mysub.py
In the root, I have a single .py file, called myprog.py :
#file .\myprog.py
from functions import *
hello("Hi from Main")
In the functions folder I have two files, init.py, myfunctions.py :
#The File: functions\__init__.py :
from myfunctions import *
#The File: functions\myfunctions.py :
def hello(sometext):
print sometext
And finally, in the subfolder, I have :
#The File: subfolder\mysub.py :
from ..functions import *
hello("Hi From mysubprogram")
The myprog.py executes fine (when running python.exe myprog.py from the parent folder), printing "Hi From Main", however, the mysub.py (when executed from the subfolder) keeps putting the error: ValueError: Attempted relative import in non-package
I have tried varying combinations in mysub.py such as from ..functions.myfunctions import * yet none yields the desired result.
I have read a few relevant articles :
using __init__.py
How to import classes defined in __init__.py
http://docs.python.org/2/tutorial/modules.html#packages-in-multiple-directories
But just can't figure this out. Oh, and once I get this working, I would like to remove the import *'s wherever possible, however, I'd rather not have to put the full paths to the hello function each time it's called, so any advise there or on cleaning up the init.py (using all or in another manner) would be a bonus.
Thanks Blckknght EDIT, I also found the below :
Relative imports for the billionth time
Which, if what I'm requesting isn't possible, perhaps I'm asking the wrong thing. If this is just outright bad practice, is the right way to accomplish my goal using sys.path or is there something else someone can recommend (like not calling functions from ../folders) ?
I think the issue has to do with how you are running the mysub.py script. Python doesn't tend to do well with scripts in packages, since the main script module is always named __main__ rather than its usual name.
I think you can fix this by running mysub with python -m subfolder.mysub, or by manipulating the __package__ variable in mysub.py (as described by PEP 366). It's not neat, unfortunately.
I'm trying to generate some LaTeX code which from thereon should generate PDF documents.
Currently, I'm using the Django templating system for dynamically creating the code, but I have no idea on as how to move on from here. I understand that I could save the code in a .tex file, and use subprocess to run pdflatex for generating the PDF. But I had so much trouble escaping the LaTeX code in "plain" Python that I decided to use the Django templating system. Is there a way that I could somehow maybe pipe the output produced by Django to pdflatex? The code produced is working properly, it's just that I do not know what to do with it.
Thanks in advance
I was tackling the same issue in a project I had previously worked on, and instead of piping the output, I created temporary files in a temporary folder, since I was worried about handling the intermediate files LaTeX produces. This is the code I used (note that it's a few years old, from when I was still new to Python/Django; I'm sure I could come up with something better if I was writing this today, but this definitely worked for me):
import os
from subprocess import call
from tempfile import mkdtemp, mkstemp
from django.template.loader import render_to_string
# In a temporary folder, make a temporary file
tmp_folder = mkdtemp()
os.chdir(tmp_folder)
texfile, texfilename = mkstemp(dir=tmp_folder)
# Pass the TeX template through Django templating engine and into the temp file
os.write(texfile, render_to_string('tex/base.tex', {'var': 'whatever'}))
os.close(texfile)
# Compile the TeX file with PDFLaTeX
call(['pdflatex', texfilename])
# Move resulting PDF to a more permanent location
os.rename(texfilename + '.pdf', dest_folder)
# Remove intermediate files
os.remove(texfilename)
os.remove(texfilename + '.aux')
os.remove(texfilename + '.log')
os.rmdir(tmp_folder)
return os.path.join(dest_folder, texfilename + '.pdf')
The dest_folder variable is usually set to somewhere in the media directory, so that the PDF can then be served statically. The value returned is the path to the file on disk. The logic of what its URL would be is handled by whatever function sets the dest_folder.