We Keep Coding

Python gsl_vector_set

I'm trying to initialize two vectors in memory using gsl_vector_set(). In the main code it is initialized to zero on default, but I wanted to initialize them to some non-zero value. I made a test code based on a working function that uses the gsl_vector_set() function.
from ctypes import *;
gsl = cdll.LoadLibrary('libgsl-0.dll');
gsl.gsl_vector_get.restype = c_double;
gsl.gsl_matrix_get.restype = c_double;
gsl.gsl_vector_set.restype = c_double;
foo = dict(
x_ht = [0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,
0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0],
x_ht_m = [0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,
0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0]
);
for f in range(0,18):
gsl.gsl_vector_set(foo['x_ht_m'],f,c_double(1.0));
gsl.gsl_vector_set(foo['x_ht'],f,c_double(1.0));
When I run the code I get this error.
ArgumentError: argument 1: <type 'exceptions.TypeError'>: Don't know how to convert parameter 1
I'm new to using ctypes and gsl functions so I'm not sure what the issue is or what the error message means. I an also not sure if there is a better way that I should be trying to save a vector to memory

Thank you #CristiFati for pointing out that I needed gsl_vector_calloc in my test code. I noticed that in the main code I was working in that the vector I needed to set was
NAV.KF_dictnry['x_hat_m']
instead of
NAV.KF_dictnry['x_ht_m']
So I fixed the test code to mirror the real code a bit better by creating a class holding the dictionary, and added the ability to change each value in the vector to an arbitrary value.
from ctypes import *;
gsl = cdll.LoadLibrary('libgsl-0.dll');
gsl.gsl_vector_get.restype = c_double;
gsl.gsl_matrix_get.restype = c_double;
gsl.gsl_vector_set.restype = c_double;
class foo(object):
fu = dict(
x_hat = gsl.gsl_vector_calloc(c_size_t(18)),
x_hat_m = gsl.gsl_vector_calloc(c_size_t(18)),
);
x_ht = [1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0]
x_ht_m = [1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0]
for f in range(0,18):
gsl.gsl_vector_set(foo.fu['x_hat_m'],f,c_double(x_ht_m[f]));
gsl.gsl_vector_set(foo.fu['x_hat'],f,c_double(x_ht[f]));
After running I checked with:
gsl.gsl_vector_get(foo.fu['x_hat_m'],0)
and got out a 1.0 (worked for the entire vector).
Turned out to just be some stupid mistakes on my end.
Thanks again!

Error with quantifier in Z3Py

I would like Z3 to check whether it exists an integer t that satisfies my formula. I'm getting the following error:
Traceback (most recent call last):
File "D:/z3-4.6.0-x64-win/bin/python/Expl20180725.py", line 18, in <module>
g = ForAll(t, f1(t) == And(t>=0, t<10, user[t].rights == ["read"] ))
TypeError: list indices must be integers or slices, not ArithRef
Code:
from z3 import *
import random
from random import randrange
class Struct:
def __init__(self, **entries): self.__dict__.update(entries)
user = [Struct() for i in range(10)]
for i in range(10):
user[i].uid = i
user[i].rights = random.choice(["create","execute","read"])
s=Solver()
f1 = Function('f1', IntSort(), BoolSort())
t = Int('t')
f2 = Exists(t, f1(t))
g = ForAll(t, f1(t) == And(t>=0, t<10, user[t].rights == ["read"] ))
s.add(g)
s.add(f2)
print(s.check())
print(s.model())

You are mixing and matching Python and Z3 expressions, and while that is the whole point of Z3py, it definitely does not mean that you can mix/match them arbitrarily. In general, you should keep all the "concrete" parts in Python, and relegate the symbolic parts to "z3"; carefully coordinating the interaction in between. In your particular case, you are accessing a Python list (your user) with a symbolic z3 integer (t), and that is certainly not something that is allowed. You have to use a Z3 symbolic Array to access with a symbolic index.
The other issue is the use of strings ("create"/"read" etc.) and expecting them to have meanings in the symbolic world. That is also not how z3py is intended to be used. If you want them to mean something in the symbolic world, you'll have to model them explicitly.
I'd strongly recommend reading through http://ericpony.github.io/z3py-tutorial/guide-examples.htm which is a great introduction to z3py including many of the advanced features.
Having said all that, I'd be inclined to code your example as follows:
from z3 import *
import random
Right, (create, execute, read) = EnumSort('Right', ('create', 'execute', 'read'))
users = Array('Users', IntSort(), Right)
for i in range(10):
users = Store(users, i, random.choice([create, execute, read]))
s = Solver()
t = Int('t')
s.add(t >= 0)
s.add(t < 10)
s.add(users[t] == read)
r = s.check()
if r == sat:
print s.model()[t]
else:
print r
Note how the enumerated type Right in the symbolic land is used to model your "permissions."
When I run this program multiple times, I get:
$ python a.py
5
$ python a.py
9
$ python a.py
unsat
$ python a.py
6
Note how unsat is produced, if it happens that the "random" initialization didn't put any users with a read permission.

How to use the R 'with' operator in rpy2

I am doing an ordinal logistic regression, and following the guide here for the analysis: R Data Analysis Examples: Ordinal Logistic Regression
My dataframe (consult) looks like:
n raingarden es_score consult_case
garden_id
27436 7 0 3 0
27437 1 0 0 1
27439 1 1 1 1
37253 1 0 3 0
37256 3 0 0 0
I am at the part where I need to to create graph to test the proportional odds assumption, with the command in R as follows:
(s <- with(dat, summary(es_score ~ n + raingarden + consult_case, fun=sf)))
(es_score is an ordinal ranked score with values between 0 - 4; n is an integer; raingarden and consult_case, binary values of 0 or 1)
I have the sf function:
sf <- function(y) {
c('Y>=1' = qlogis(mean(y >= 1)),
'Y>=2' = qlogis(mean(y >= 2)),
'Y>=3' = qlogis(mean(y >= 3)))
}
in a utils.r file that I access as follows:
from rpy2.robjects.packages import STAP
with open('/file_path/utils.r', 'r') as f:
string = f.read()
sf = STAP(string, "sf")
And want to do something along the lines of:
R = ro.r
R.with(work_case_control, R.summary(formula, fun=sf))
The major problem is that the R withoperator is seen as a python keyword, so that even if I access it with ro.r.with it is still recognized as a python keyword. (As a side note: I tried using R's apply method instead, but got an error that TypeError: 'SignatureTranslatedAnonymousPackage' object is not callable ... I assume this is referring to my function sf?)
I also tried using the R assignment methods in rpy2 as follows:
R('sf = function(y) { c(\'Y>=1\' = qlogis(mean(y >= 1)), \'Y>=2\' = qlogis(mean(y >= 2)), \'Y>=3\' = qlogis(mean(y >= 3)))}')
R('s <- with({0}, summary(es_score~raingarden + consult_case, fun=sf)'.format(consult))
but ran into issues where the dataframe column names were somehow causing the error: RRuntimeError: Error in (function (file = "", n = NULL, text = NULL, prompt = "?", keep.source = getOption("keep.source"), :
<text>:1:19: unexpected symbol
1: s <- with( n raingarden
I could of course do this all in R, but I have a very involved ETL script in python, and would thus prefer to keep everything in python using rpy2 (I did try this using mord for scipy-learn to run my regreession, but it is pretty primitive).
Any suggestions would be most welcome right now.
EDIT
I tried various combinations #Parfait's suggestions, and qualifying the fun argument is syntactically incorrect, as per PyCharm interpreter (see image with red highlighting at end): ... it doesn't matter what the qualifier is, either, I always get an error
that SyntaxError: keyword can't be an expression.
On the other hand, with no qualifier, there is no syntax error: , but I do get the error TypeError: 'SignatureTranslatedAnonymousPackage' object is not callable when using the function sf as obtained:
from rpy2.robjects.packages import STAP
with open('/Users/gregsilverman/development/python/rest_api/rest_api/scripts/utils.r', 'r') as f:
string = f.read()
sf = STAP(string, "sf")
With that in mind, I created a package in R with the function sf, imported it, and tried various combos with the only one producing no error, being: print(base._with(consult_case_control, R.summary(formula, fun=gms.sf))) (gms is a reference to the package in R I made).
The output though makes no sense:
Length Class Mode
3 formula call
I am expecting a table ala the one on the UCLA site. Interesting. I am going to try recreating my analysis in R, just for the heck of it. I still would like to complete it in python though.

Consider bracketing the with call and be sure to qualify all arguments including fun:
ro.r['with'](work_case_control, ro.r.summary(formula, ro.r.summary.fun=sf))
Alternatively, import R's base package. And to avoid conflict with Python's named method with() translate the R name:
from rpy2.robjects.packages import importr
base = importr('base', robject_translations={'with': '_with'})
base._with(work_case_control, ro.r.summary(formula, ro.r.summary.fun=sf))
And be sure to properly create your formula. Consider using R's stats packages' as.formula to build from string. Notice too another translation is made due to naming conflict:
stats = importr('stats', robject_translations={'format_perc': '_format_perc'})
formula = stats.as_formula('es_score ~ n + raingarden + consult_case')

Python: cannot import name x for importing module

** EDIT: Copy-pasting my actual file to ease confusion. The code snippet below is in a file named train_fm.py:
def eval_fm(x,b,w,V):
# evaluate a degree 2 FM. x is p X B
# V is p x k
# some python code that computes yhat
return(yhat);
Now in my main file: I say the following
from train_fm import eval_fm
and I get the error:
ImportError: cannot import name f1
When I type
from train_fm import train_fm
I do not get an error.
OLD QUESTION BELOW :
def train_fm(x,y,lb,lw,lv,k,a,b,w,V):
# some code
yhat = eval_fm(x,b,w,V);
# OUTPUTS
return(b,w,V);
I have a file called f2.py, where I define 2 functions (note that one of the functions has the same name as the file)
def f1():
some stuff;
return(stuff)
def f2():
more stuff;
y = f1();
return(y)
In my main file, I do
from aaa import f1
from aaa import f2
but when I run the first of the 2 commands above, I get
ImportError: cannot import name f1
Any idea what is causing this? The second function gets imported fine.

Generating LaTeX tables from R summary with RPy and xtable

I am running a few linear model fits in python (using R as a backend via RPy) and I would like to export some LaTeX tables with my R "summary" data.
This thread explains quite well how to do it in R (with the xtable function), but I cannot figure out how to implement this in RPy.
The only relevant thing searches such as "Chunk RPy" or "xtable RPy" returned was this, which seems to load the package in python but not to use it :-/
Here's an example of how I use RPy and what happens.
And this would be the error without bothering to load any data:
from rpy2.robjects.packages import importr
xtable = importr('xtable')
latex = xtable('')
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-131-8b38f31b5bb9> in <module>()
----> 1 latex = xtable(res_sum)
2 print latex
TypeError: 'SignatureTranslatedPackage' object is not callable
I have tried using the stargazer package instead of xtable and I get the same error.

Ok, I solved it, and I'm a bit ashamed to say that it was a total no-brainer.
You just have to call the functions as xtable.xtable() or stargazer.stargazer().

To easily generate TeX data from Python, I wrote the following function;
import re
def tformat(txt, v):
"""Replace the variables between [] in raw text with the contents
of the named variables. Between the [] there should be a variable name,
a colon and a formatting specification. E.g. [smin:.2f] would give the
value of the smin variable printed as a float with two decimal digits.
:txt: The text to search for replacements
:v: Dictionary to use for variables.
:returns: The txt string with variables substituted by their formatted
values.
"""
rx = re.compile(r'\[(\w+)(\[\d+\])?:([^\]]+)\]')
matches = rx.finditer(txt)
for m in matches:
nm, idx, fmt = m.groups()
try:
if idx:
idx = int(idx[1:-1])
r = format(v[nm][idx], fmt)
else:
r = format(v[nm], fmt)
txt = txt.replace(m.group(0), r)
except KeyError:
raise ValueError('Variable "{}" not found'.format(nm))
return txt
You can use any variable name from the dictionary in the text that you pass to this function and have it replaced by the formatted value of that variable.
What I tend to do is to do my calculations in Python, and then pass the output of the globals() function as the second parameter of tformat:
smin = 235.0
smax = 580.0
lst = [0, 1, 2, 3, 4]
t = r'''The strength of the steel lies between SI{[smin:.0f]}{MPa} and \SI{[smax:.0f]}{MPa}. lst[2] = [lst[2]:d].'''
print tformat(t, globals())
Feel free to use this. I put it in the public domain.
Edit: I'm not sure what you mean by "linear model fits", but might numpy.polyfit do what you want in Python?

To resolve your problem, please update stargazer to version 4.5.3, now available on CRAN. Your example should then work perfectly.