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Maybe the question is dumb, but so far I have not been able to find a solution.
I have been handed a code from other person who was working probably with a different set than mine (e.g. Python 2 instead of 3, etc).
So I have done some small changes to make things work, but I am stuck in a probably simple problem related to h5py.
The part of the code where it crushes looks like:
labels_ALL = ['ionic_str','psi0','psi1','psi2','psid','zeta','sig0','sig1','sig2','sigd','sig0_eq','sig1_eq','sig2_eq','sigd_eq','ch_bal_EDL','ch_bal_aq', 'sum_resid']
units_ALL = ['(mol/L)','(V)','(V)','(V)','(V)','(V)','(C/m**2)','(C/m**2)','(C/m**2)','(C/m**2)','(mol(eq))','(mol(eq))','(mol(eq))','(mol(eq))','(C/m**2)','(mol(eq)/L)',' ']
for i in range(len(Labels)):
labels_ALL.append(Labels[i])
units_ALL.append('(mol/L)')
base.create_dataset('Labels', data=labels_ALL)
base.create_dataset('Units', data=units_ALL)
The problem seems to be in base.create_dataset:
Traceback (most recent call last):
File "C:\Users\DaniJ\Documents\PostDoc_Jena\Trips, Conf, etc\Sinfonia Workshop\Exercise_1\exercise_1_SINFONIA_for_One\NR_chem_SINGLE_NoEu.py", line 252, in <module>
base.create_dataset('Labels', data=labels_ALL)
File "C:\Users\DaniJ\anaconda3\lib\site-packages\h5py\_hl\group.py", line 136, in create_dataset
dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
File "C:\Users\DaniJ\anaconda3\lib\site-packages\h5py\_hl\dataset.py", line 118, in make_new_dset
tid = h5t.py_create(dtype, logical=1)
File "h5py\h5t.pyx", line 1634, in h5py.h5t.py_create
File "h5py\h5t.pyx", line 1656, in h5py.h5t.py_create
File "h5py\h5t.pyx", line 1717, in h5py.h5t.py_create
TypeError: No conversion path for dtype: dtype('<U10')
the variable base seems to be a h5py._hl.files.File variable.
Does somebody how can I solve this problem?
Thanks
Best regards,
Dani
Did you solve your problem? I'm 99.9% sure it's related to your Labels data -- likely it's in a NumPy array instead of a List. I wrote 3 short examples to demonstrate the difference.
The first code segment uses a List and successfully creates the
datasets in file SO_69900543_1.h5.
The second code segment reproduces your error. It converts the List
to a NumPy Array then fails when attempting to create the datasets
in file SO_69900543_2.h5. Notice that it gives the same error
message you encountered: TypeError: No conversion path for dtype: dtype('<U10').
The third code segment shows how to modify numpy.str_ elements to str (solves problem in segment #2). Note that the each Labels value is converted with str() before it is added to Labels_All.
Maybe this will help you find (and fix) your problem with Unicode data.
Code segment 1 (works):
Labels = ['H+','Na+','Cl-','OH-','>SOH_x','>SO-_x','>SONa_x','>SOH2+_x','>SOH2Cl_x','>SOH_y','>SO-_y','>SONa_y']
labels_ALL = ['ionic_str','psi0','psi1','psi2','psid','zeta','sig0','sig1','sig2','sigd','sig0_eq','sig1_eq','sig2_eq','sigd_eq','ch_bal_EDL','ch_bal_aq', 'sum_resid']
units_ALL = ['(mol/L)','(V)','(V)','(V)','(V)','(V)','(C/m**2)','(C/m**2)','(C/m**2)','(C/m**2)','(mol(eq))','(mol(eq))','(mol(eq))','(mol(eq))','(C/m**2)','(mol(eq)/L)',' ']
for i in range(len(Labels)):
labels_ALL.append(Labels[i])
units_ALL.append('(mol/L)')
with h5py.File('SO_69900543_1.h5','w') as base:
base.create_dataset('Labels', data=labels_ALL)
base.create_dataset('Units', data=units_ALL)
Code segment 2 (returns TypeError):
Labels = ['H+','Na+','Cl-','OH-','>SOH_x','>SO-_x','>SONa_x','>SOH2+_x','>SOH2Cl_x','>SOH_y','>SO-_y','>SONa_y']
# Convert Labels List to NumPy array
# This will trigger the error when creating the dataset
Labels = np.array(Labels)
labels_ALL = ['ionic_str','psi0','psi1','psi2','psid','zeta','sig0','sig1','sig2','sigd','sig0_eq','sig1_eq','sig2_eq','sigd_eq','ch_bal_EDL','ch_bal_aq', 'sum_resid']
units_ALL = ['(mol/L)','(V)','(V)','(V)','(V)','(V)','(C/m**2)','(C/m**2)','(C/m**2)','(C/m**2)','(mol(eq))','(mol(eq))','(mol(eq))','(mol(eq))','(C/m**2)','(mol(eq)/L)',' ']
for i in range(len(Labels)):
labels_ALL.append(Labels[i])
units_ALL.append('(mol/L)')
for i in range(len(labels_ALL)):
print(i, type(labels_ALL[i]), type(units_ALL[i]))
with h5py.File('SO_69900543_2.h5','w') as base:
base.create_dataset('Labels', data=labels_ALL)
base.create_dataset('Units', data=units_ALL)
Code segment 3 (works):
Labels = ['H+','Na+','Cl-','OH-','>SOH_x','>SO-_x','>SONa_x','>SOH2+_x','>SOH2Cl_x','>SOH_y','>SO-_y','>SONa_y']
# Convert Labels List to NumPy array
# This will trigger the error when creating the dataset if not modified
Labels = np.array(Labels)
labels_ALL = ['ionic_str','psi0','psi1','psi2','psid','zeta','sig0','sig1','sig2','sigd','sig0_eq','sig1_eq','sig2_eq','sigd_eq','ch_bal_EDL','ch_bal_aq', 'sum_resid']
units_ALL = ['(mol/L)','(V)','(V)','(V)','(V)','(V)','(C/m**2)','(C/m**2)','(C/m**2)','(C/m**2)','(mol(eq))','(mol(eq))','(mol(eq))','(mol(eq))','(C/m**2)','(mol(eq)/L)',' ']
for i in range(len(Labels)):
# use str() to convert from 'numpy.str_' to 'str'
labels_ALL.append(str(Labels[i]))
units_ALL.append('(mol/L)')
for i in range(len(labels_ALL)):
print(i, type(labels_ALL[i]), type(units_ALL[i]))
with h5py.File('SO_69900543_2.h5','w') as base:
base.create_dataset('Labels', data=labels_ALL)
base.create_dataset('Units', data=units_ALL)
I am trying to implement my own version of the MatLab function imhmin() in Python using OpenCV and (naturally) NumPy. If you are not familiar with this MatLab function, it's extremely useful for segmentation. MatLab's documentation can explain it much better than I can:
https://it.mathworks.com/help/images/ref/imhmin.html
Here is what I have so far:
(For the sake of keeping this short, I did not include the local_min function. It takes one image parameter and returns an image of the same size where local minima are 1s and everything else is 0.)
from volume import show
import cv2
import numpy
def main():
arr = numpy.array( [[5,5,5,5,5,5,5],
[5,0,3,1,4,2,5],
[5,5,5,5,5,5,5]] ) + 1
res = imhmin(arr, 3)
print(res)
def imhmin(src, h):
# TODO: speed up function by cropping image
edm = src.copy()
# d is the domain / all values contained in the array
d = numpy.unique(edm)
# for the index of each local minima (sorted gtl)
indices = numpy.nonzero(local_min(edm)) # get indices
indices = numpy.dstack((indices[0], indices[1]))[0].tolist() # zip
# sort based on the value of edm[] at that index
indices.sort(key = lambda _: edm[_[0],_[1]], reverse = True)
for (x,y) in indices:
start = edm[x,y] # remember original value of minima
# for each in a list of heights greater than the starting height
for i in range(*numpy.where(d==edm[x,y])[0], d.shape[0]-1):
# prevent exceeding target height
step = start + h if (d[i+1] - start > h) else d[i+1]
#-------------- WORKS UNTIL HERE --------------#
# complete floodFill syntax:
# cv2.floodFill(image, mask, seed, newVal[, loDiff[, upDiff[, flags]]]) → retval, rect
# fill UPWARD onto image (and onto mask?)
cv2.floodFill(edm, None, (y,x), step, 0, step-d[i], 4)
# fill DOWNWARD NOT onto image
# have you overflowed?
if __name__ == "__main__":
main()
Which works fine until it gets to the floodfill line. It barks this error back:
Traceback (most recent call last):
File "edm.py", line 94, in <module>
main()
File "edm.py", line 14, in main
res = imhmin(arr, 3)
File "edm.py", line 66, in imhmin
cv2.floodFill(edm, None, (y,x), step, 0, step-d[i], 4)
TypeError: Layout of the output array image is incompatible with cv::Mat (step[ndims-1] != elemsize or step[1] != elemsize*nchannels)
At first I thought maybe the way I laid out the parameters was wrong because of the stuff about step in the traceback, but I tried changing that variable's name and have come to the conclusion that step is some variable name in OpenCV's code. It's talking about the output array, and I'm not using a mask, so something must be wrong with the array edm.
I can suppress this error by replacing the floodfill line with this one:
cv2.floodFill(edm.astype(numpy.double), None, (y,x), step, 0, step-d[i], 4)
The difference being that I am typecasting the numpy array to a float array. Then I am left with this error:
Traceback (most recent call last):
File "edm.py", line 92, in <module>
main()
File "edm.py", line 14, in main
res = imhmin(arr, 3)
File "edm.py", line 64, in imhmin
cv2.floodFill(edm.astype(numpy.double), None, (y,x), step, 0, step-d[i], 4)
TypeError: Scalar value for argument 'newVal' is not numeric
This is where I started suspecting something was seriously wrong, because step is "obviously" going to be an integer here (maybe it isn't obvious, but I did try printing it and it looks like it's just an integer, not an array of one integer or anything weird like that).
To entertain the error message, I typecast the newVal parameter to a float. I got pretty much the exact same error message about the upDiff parameter, so I just typecast that too, resulting in this line of code:
cv2.floodFill(edm.astype(numpy.double), None, (y,x), float(step), 0, float(step-d[i]), 4)
I know this isn't how I want to be doing things, but I just wanted to see what would happen. What happened was I got this scary looking error:
Traceback (most recent call last):
File "edm.py", line 92, in <module>
main()
File "edm.py", line 14, in main
res = imhmin(arr, 3)
File "edm.py", line 64, in imhmin
cv2.floodFill(edm.astype(numpy.double), None, (y,x), float(step), 0, float(step-d[i]), 4)
cv2.error: OpenCV(3.4.2) /opt/concourse/worker/volumes/live/9523d527-1b9e-48e0-7ed0-a36adde286f0/volume/opencv-suite_1535558719691/work/modules/imgproc/src/floodfill.cpp:587: error: (-210:Unsupported format or combination of formats) in function 'floodFill'
I don't even know where to start with this. I've used OpenCV's floodfill function many times before and have never run into problems like this. Can anyone provide any insight?
Thanks in advance
Antonio
I have built a code for a codewars problem. I think it is correct but it shows me an error I don't understand.
Can you tell me what am I doing wrong?
import math
def waterbombs(fire, w):
s=""
countx=0
for i in fire:
if i=="x":
countx+=1
elif i=="Y":
countx=0
return sum(math.ceil(countx/w))
waterbombs("xxYxx", 3)
This is the error:
Traceback (most recent call last):
File "D:\Curso Python Pildorasinformaticas\Ejercicios Codewars\Aerial Firefighting.py", line 16, in <module>
waterbombs("xxYxx", 3)
File "D:\Curso Python Pildorasinformaticas\Ejercicios Codewars\Aerial Firefighting.py", line 13, in waterbombs
return sum(math.ceil(countx/w))
TypeError: 'int' object is not iterable
[Finished in 0.2s]
Why are you doing sum(math.ceil(countx/w)) ?
What is the objective of the sum method here, since there is only value returned by math.ceil ?
The sum would throw that error if you pass a single value to it. You're supposed to pass a list of values of the sum method.
For eg: sum(5) would give you the same error you see above, but sum([5]) would return you 5.
I'm trying to create a GUI for a signal analysis simulation that i'm writing in Python. For that, I use AppJar. However, when I call the function that generates the signal, I get a ValueError like in the title.
I've read every single ValueError post on stackOverflow (i could have missed one maybe, but i did my best) and all of them are about extra spacings, letters that can not be parsed as a floating point number, etc. None of that seems to apply here.
Basically, i'm using this code to call a function to generate my signal:
signal_axes = app.addPlot("signal", *logic.signal(5, 2), 0, 0, 1)
And the relevant part of the function itself (in the file logic.py, which is imported)
def signal(electrodes, length):
velocity = math.sqrt((3.2e-19 * kinetic_energy) / (mass * 1.66e-27))
frequency = velocity / length
This is not the whole function, the variables are all declared and unused variables are used later in the function.
The error specifically points to the line with "frequency = velocity / length", telling me:
TypeError: unsupported operand type(s) for /: 'float' and 'str'
When i try to fix it by using "float(length)" i get the error:
ValueError: could not convert string to float:
In one of the answers on StackExchange someone suggested using .strip() to get rid of invisible spaces. So i tried using:
length.strip()
But that gives me the following error:
AttributeError: 'float' object has no attribute 'strip'
I am slowly descending into madness here. The following code, by the way, stand-alone, works:
import numpy as np
kinetic_energy = 9000
mass = 40
length = 2e-2
velocity = np.sqrt((3.2e-19 * kinetic_energy) / (mass * 1.66e-27))
frequency = float(velocity) / float(length)
print(frequency)
Can anyone see what could be wrong? I've included all the relevant code below, it's not my complete file but this alone should give an output, at least.
run.py
import logic
from appjar import gui
def generate(btn):
app.updatePlot("signal", *logic.signal(app.getEntry("electrodes"), app.getEntry("length")))
showSignalLabels()
def showSignalLabels():
signal_axes.set_xlabel("time (us)")
signal_axes.set_ylabel("amplitude (uV)")
app.refreshPlot("signal")
app = gui()
signal_axes = app.addPlot("signal", *logic.signal(5, 0.02), 0, 0, 1)
app.addLabelEntry("electrodes", 1, 0, 1)
app.addLabelEntry("length", 2, 0, 1)
showSignalLabels()
app.addButton("Generate", generate)
app.go()
logic.py
import numpy as np
import math
import colorednoise as cn
steps = 5000
amplitude = 1
offset_code = 0
kinetic_energy = 9000
mass = 40
centered = 1
def signal(electrodes, length):
velocity = math.sqrt((3.2e-19 * kinetic_energy) / (mass * 1.66e-27))
frequency = velocity / length
time = 2 * (electrodes / frequency)
--- irrelevant code ---
return OutputTime, OutputSignal
edit: here is the full traceback.
Exception in Tkinter callback
Traceback (most recent call last):
File "E:\Internship IOM\WPy64-3720\python-3.7.2.amd64\lib\tkinter\__init__.py", line 1705, in __call__
return self.func(*args)
File "E:\Internship IOM\PythonScripts\appJar\appjar.py", line 3783, in <lambda>
return lambda *args: funcName(param)
File "E:/Internship IOM/PythonScripts/appJar/testrun.py", line 12, in generate
app.updatePlot("signal", *logic.signal(app.getEntry("electrodes"), app.getEntry("length")))
File "E:\Internship IOM\PythonScripts\appJar\logic.py", line 33, in signal
frequency = velocity / length
TypeError: unsupported operand type(s) for /: 'float' and 'str'
You should convert at the calling site, i.e. do:
def generate(btn):
app.updatePlot("signal", *logic.signal(app.getEntry("electrodes"),
float(app.getEntry("length"))))
...
Because otherwise your function logic.signal receives different type (str and float). That's why you receive the other error about float has no strip because somewhere else in your code you do:
signal_axes = app.addPlot("signal", *logic.signal(5, 0.02), 0, 0, 1)
Here you pass it a float.
Since your original error was could not convert string to float with an apparently empty string, you need to take an extra measure to prevent empty values from the app. You can use a try ... except:
def generate(btn):
try:
length = float(app.getEntry("length"))
except ValueError:
# Use some default value here, or re-raise.
length = 0.
app.updatePlot("signal", *logic.signal(app.getEntry("electrodes"), length))
I am trying to find the laplace inverse of an expression for which all but one variable are already defined at the time of declaration:
from numpy import *
import mpmath as mp
p0 = 1
E = 2
c= 3
L = 4
x = 2.5
t = linspace(1,5,10)
ulaplace = []
def U(s):
return(c*p0*(-exp(L*s/c) + exp(s*(L + 2*x)/c))*exp(-s*x/c)/(E*s**2*(exp(2*L*s/c) + 1)))
for ti in t:
ulaplace.append(mp.invertlaplace(U, ti, method='talbot'))
But I am getting this error:
Traceback (most recent call last):
File "D:\TEMP\IDLEscripts\CompareAnalyticalSolutions2.py", line 46, in <module>
ulaplace.append(mp.invertlaplace(U, ti, method='talbot'))
File "C:\Python35\lib\site-packages\mpmath\calculus\inverselaplace.py", line 805, in invertlaplace
fp = [f(p) for p in rule.p]
File "C:\Python35\lib\site-packages\mpmath\calculus\inverselaplace.py", line 805, in <listcomp>
fp = [f(p) for p in rule.p]
File "D:\TEMP\IDLEscripts\CompareAnalyticalSolutions2.py", line 43, in U
return(c*p0*(-exp(L*s/c) + exp(s*(L + 2*x)/c))*exp(-s*x/c)/(E*s**2*(exp(2*L*s/c) + 1)))
TypeError: attribute of type 'int' is not callable
I also tried the lambda function format suggested by the doc website but still got the same error.
Does the mpmath.invertlaplace function require that everything be in numerical termsat the time of definition? I am asking because this worked:
>>> import mpmath as mp
>>> def F(s):
return 1/s
>>> mp.invertlaplace(F,5, method = 'talbot')
mpf('1.0')
If so, I need to be able to circumvent this. The whole point for me is to play around with the other variables and see how they affect the inverse laplacian. Furthermore one would think that the function gets evaluated before it is passed on to mpmath.
If not, then what on earth is going on here?
Allright I got it. Basically the function that mp.invertlaplace needs to itself only use mpmath defined functions. In the code provided in the original question I am using exp from the numpy library. So exp(x) is really numpy.exp(x). To make the code work it needs to call the mpmath.exp function as follows:
def U(s):
return -p0*mp.exp(s*x/c)/(E*s*(-s*mp.exp(L*s/c)/c - s*mp.exp(-L*s/c)/c)) + p0*mp.exp(-s*x/c)/(E*s*(-s*mp.exp(L*s/c)/c - s*mp.exp(-L*s/c)/c))
I have not tested the above on the reduced example I provided in the original question, since it is a subset of the more general script. However it should work and this appears to be the root of the problem.