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Which Machine learning algorithms suits best in the material science for the problems that aims to determine the properties and functions of existing materials. Eg. typical problem of determination of band gap of solar cell materials using ML.
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Random forest, Support vector machine and Gradient Boosting Machines
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Hello everyone,
I am currently exploring several options to give the collected data the greatest value possible.
I have demographic data on older people, where I perform various memory and mood tests. The previous hypotheses were the following:
  • Drawing out the difference between dementia and depression.
  • Identify if the digital tool is as effective as the classic one
  • Contributing to the data collected as a predictor of dementia
A few years ago, studies talked about the real possibility of predicting some years before, what your future mental health will be in terms of memory.
Do you think there is any way to provide value in that sense, with demographic data, clinical tests like MoCa, Yesavage, Lawton, MFE?
Here you are some of these studies.
Study of the brain through images:
  • Jagust, W. (2018). Images of the evolution and pathophysiology of Alzheimer's disease. Nature Reviews. Neuroscience, 19(11), 687–700. doi:10.1038/s41583-018-0067-3.
Analysis of biomarkers in cerebrospinal fluid or blood:
  • Hampel, H., O'Bryant, S. E., Castrillo, J. I., Ritchie, C., Rojkova, K., Broich, K.,… Lista, S. (2018). PRECISION MEDICINE – The golden door for the detection, treatment and prevention of Alzheimer's disease. Journal of Alzheimer's Disease Prevention, 5(4), 243–259. doi:10.14283/jpad.2018.29.
Genetic studies:
  • Karch, C. M., and Goate, A. M. (2015). Alzheimer's disease risk genes and mechanisms of disease pathogenesis. Biological Psychiatry, 77 (1), 43–51. doi:10.1016/j.biopsych.2014.05.006.
Cognitive evaluations and neuropsychological tests:
  • Amariglio, R. E., Becker, J. A., Carmasin, J., Wadsworth, L. P., Lorius, N., Sullivan, C.,… Sperling, R. A. (2012). Subjective cognitive complaints and amyloid burden in cognitively normal older people. Neuropsychology, 50(12), 2880–2886. doi:10.1016/j.neuropsychologia.2012.08.011.
With python and with sk-learn is a best way to start?
Which features are the more relevants to add value to the prediction?
Thanks in advance,
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Thanks Adnan Majeed ,
There are important ethic considerations as you mention.
In our use case, the digitalized clinical tests, dementia and depression test, are administered. We use Alexa devices to pass these tests so that the information is digitized, obtaining the answer of the final score automatically.
Taking into account the data collected from our users, the features to clasify them will be:
  • Demographic Data
  • Behavior patterns
  • Their answer to the clinical test
  • Voice Data or voice patterns
  • Gesture patterns
My proposal is to compare the digitized test with the classic one to check the sensitivity and specificity. And compare these two terms with the ones I get when I add the Machine Learning layer. Probably the library I use is Scikit-learn.
Do you think I'm on the right path? Are there any important suggestions to keep in mind?
Thanks in advance,
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I have processed the quad-pol SAR data using POLSARPRO tool, followed by matlab. Now to cross verify my results, I am looking for code in Python or Matlab to read the vv polarized file in .grd or .mlc format, followed by basic radiometric correction.
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import numpy as np # Replace with your file pathfilename = "path/to/uavsar.grd" # Read data based on file format (e.g., data type, number of elements) with open(filename, "rb") as f: data = np.fromfile(f, dtype=np.float32) # Adjust data type as needed # Reshape data based on number of rows, columns, and polarization channels # (Information on these might be in a separate file or require manual parsing)data = data.reshape((rows, columns, num_channels)) # Access specific polarization channel (e.g., VV)vv_channel = data[:, :, 0] # Assuming VV is the first channel (adjust indexing) # Further processing and analysis of the data
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So I am conducting a research on changes in NO2 and aerosol index during a certain time period of 1 year. I am using sentinel-5 data. Following is the link:
I used anaconda(spyder) to analyze the data, creating a map for each day. So in total, there are like more than 30 images. A made a collage of these for my manuscript but it doesn't look quite neat. And is a bit difficult to comprehend.
Is there any way I can integrate these images into one i.e. one image per month that reveals the average. Any tool or software that is acceptable for research purpose. I really need help with this.
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With one year of image data on NO2 and aerosols, you can produce much more specific statistics than just an average yearly value per pixel.
What about P99, P95 percentiles? I figger your imagery must contain different strata, hence produce percentiles for these strata, and you will learn much more about pollution behavior than just with a yearly average value. Instead of using Matplotlib, it is better to use ENVI and Statistica combined to do the job.
#Justsaying
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Dear All,
I have an imagery with a single fish species within each image along with a list of morphometric measurements of the fish (length, width, length of tail, etc). I would like to train a CNN model that will predict these measurements having as input only the images. Any ideas what kind of architecture is ideal for this task? I read about multioutput learning, but I haven't found a practical implementation in Python.
Thank you for your time.
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Thank you Aldo for your suggestion. I can see the general framework.
Cheers!
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As a student in Bachelor degree program in computer science field we have a project in course of "Language Theory", our project related with Natural Language Processing:
- First phase talks about giving a dictionary of "Physical Objects Name's" and give it a "Text" (all this in input) after that it gives us a list of "Physical Objects Name's" in our "Text" (this is the output as a file).
- Second phase is to use the last list to as input and implement a code that can classify words by topics and the result will be the general topic or idea of our text.
In this project I did the first phase but in the second one I don't understand how can I implement my code.
P.S: I try to add a python file but I can't, so for all those who wanna help me I can send them my work.
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You can use spaCy NER (named entity recognition models) or hugging face transformers, depending on the topic each model is trained to detect.
Hope it helps,
Az
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Instead of python or R, what tools can be used to generate heat map for sequencing data?
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Hi everyone,
I'm working on a project where I need to compare the similarity between line curves on two separate charts, and I could use some guidance. Here’s the situation:
  1. First Chart Details: Contains two curves, both of which are moving averages. These curves are drawn on a browser canvas by a user. I have access to the x and y data points of these curves.
  2. Second Chart Details: Contains two curves, with accessible x and y data points. In this chart, the x-axis represents time, and the y-axis represents values.
Challenge:
  • The two charts do not share the same coordinate system values.
Goal:
  • I would like to compare the similarity in patterns between individual lines across the two charts (i.e., one line from the first chart vs. one line from the second chart).
  • Additionally, I want to compare the overall shape formed by both lines on the first chart to the shape formed by both lines on the second chart.
Could anyone provide advice on methodologies or algorithms that could help in assessing the similarity of these line curves?
Thank you for any help.
Lovro Bajc
I have attached
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Adnan Majeed Thank you for extensive answer. I am searching for Quantitative Comparison solution. I need to find similarity between shape formed by two curves on one 2D space compared to shape formed by other two curves on second 2D space.
Calculating area between two curves is not a suitable solution as the shape is not taken into consideration.
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I have amassed decades long data on bird populations and need help in calculating their population trends. There is a great bulk of research published worldwide where a variety of statistical packages (e.g TrendSpotter, rTrim here) were used to index population trends, however, I found none that would do this job using Python. While I have a profficient Python developer, the latter is having hard time deciding on the choice of appropriate statistical methods that could be used to analyse data. Anyone can help?
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try using data visualization using python because it will able to give trends. As python is able to analyze large datasets
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Greetings everyone,
I am a BTech student pursuing my bachelor's degree in Information Technology with a keen interest in machine learning. I am actively seeking mentors or co-authors for collaborative research endeavors in this domain. If you are currently engaged in research on machine learning or related topics and are open to collaboration, I would greatly appreciate it if you could reach out to me.
While I possess a solid understanding of machine learning concepts and proficiency in Python, I find myself at a juncture where I am seeking guidance on how to delve into a more focused research topic. I am enthusiastic about the prospect of working under the mentorship of experienced researchers in this field to further develop my skills and contribute meaningfully to ongoing projects.
If you are interested in exploring potential collaborations or if you have any advice to offer on initiating research in machine learning, please feel free to message me. I am eager to engage in fruitful discussions and collaborative efforts within the research community.
Thank you for your attention, and I'm excited about the prospect of collaborating and learning from fellow enthusiasts in the research community.
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Aanya Singh Dhaka I would love to connect with you, research with you and will be happy to mentor you too!
Feel free to whatsapp me at +918200713617
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I am currently implementing the following two RL algorithms for 5G
(i) Power control to maximize throughput in a multi-gNB multi-UE scenario, and
(ii) Maximizing throughput subject to delay constraints in a single-gNB multi-UE scenario
I have made significant progress using an external Python program connected to NetSim's gNB scheduler. This setup facilitates the exchange of states and rewards between the scheduler and the Python program.
I am interested in exploring scenarios with time delays in state-reward exchanges, such as delayed state reception. How does RL adapt in such situations? I would appreciate any relevant research papers on this topic
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I can start with a constant delay MDP. As regards the RL algorithm, I can start with tabular Q-Learning if that is easier
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On dftbephy code : How can we fix the problems for run python bands.py and python dftbephy-epc.py ?The problems on my system are ; bands.py line 92, dftbephy/calc.py line 176 and 253, dftbephy/epc.py line 83, dftbephy-epc.py line 138 and python/site-packages/scipy/linalg/decmpy.py line 578 there are errors which stop run. How can I resolve the issue or fix the problems as shown on screenshot file below.
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1.The numpy.linalg.LinAlgError is an exception that occurs when you're performing linear algebra operations using the NumPy library, and a mathematical condition prevents the correct execution of the operation. This error usually happens when you attempt to invert a singular matrix (a matrix that has a determinant of zero) or perform an operation that relies on matrix inversion, such as solving a system of linear equations or computing the inverse of a matrix.
2.use other versions of python for run this code , or search the best version of python for packages used in your .py file.
- Also don't forget to update the -apt.
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I am trying to plot using the attached file data file, "wan_band.dat". In the past, I also found the same error. But somehow it was resolved automatically. Again, I stuck with it. I am not able to understand the reason for the issue. The error is mentioned in the attached image, "Reshape-error.PNG".
I am using the Python code to plot using the commands as,
import matplotlib.pyplot as plt
from matplotlib import rcParamsDefault
import numpy as np
%matplotlib inline
import os # To load image/data from path. #### ##################################################################################################
plt.rcParams["figure.dpi"]=150
plt.rcParams["figure.facecolor"]="white"
plt.rcParams["figure.figsize"]=(8, 6) ################################################################################################## ##################################################################################################
data = np.loadtxt("../wannier90/wan_band.dat")
k = np.unique(data[:, 0])
bands = np.reshape(data[:, 1], (-1, len(k)))
for band in range(len(bands)):
plt.plot(k, bands[band, :], "o-", markersize=5, linewidth=2, alpha=0.8, color='b', linestyle='-')
plt.xlim(min(k), max(k))
plt.xlim(0, 3.81842), plt.ylim(-8, 8)
##################################################################################################
plt.rc('ytick',labelsize=20),
plt.rc('xtick',labelsize=20),
plt.show() ##################################################################################################
I have a guess that the error has occurred cause of "bands = np.reshape(data[:, 1], (-1, len(k)))", but not able to understand.
Please help me about the same.
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Thank you Josnier Ramos Guardarrama for your response. I have tried it, not able to work. It shows a blank plot with the error shown in the attached image.
I am using the same code mentioned by "Josnier Ramos Guardarrama".
```
import matplotlib.pyplot as plt
from matplotlib import rcParamsDefault
import numpy as np
%matplotlib inline
import os # To load image/data from path. ####
plt.rcParams["figure.dpi"]=150
plt.rcParams["figure.facecolor"]="white"
plt.rcParams["figure.figsize"]=(8, 6)
data = np.loadtxt("../wannier90/wan_band.dat")
k = np.unique(data[:, 0])
#print("data shape:", data.shape)
#print("k shape:", k.shape)
# bands = np.reshape(data[:, 1], (-1, len(k)))
bands = np.reshape(data[:, 1], (-1, data.shape[0]))
# for band in range(len(bands)):
for band in range(bands.shape[0]):
# plt.plot(k, bands[band, :]-6.6527, "o-", markersize=5, linewidth=2, alpha=0.5, color='k', linestyle='-')
plt.plot(k, bands[band, :], "o-", markersize=5, linewidth=2, alpha=0.8, color='b', linestyle='-')
plt.xlim(min(k), max(k))
# plt.xlim(0, 3.81842), plt.ylim(-8, 8)
plt.rc('ytick',labelsize=20), plt.rc('xtick',labelsize=20),
```
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A variety of package managers are available for Python, such management being essential if you're using the wide variety of Python packages available for a diversity of applications ranging from quantum physics to machine learning. Which package managers and why would be the best ones to investing time in learning how to use?
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I can recommend conda, or it's faster little brother mamba to manage (reproducible) software environments. It keeps track of separated installations of packages and these so called environments can be exported an taken to another system.
It also takes away the burden of compiling packages yourself, which rarely happens if you install via pip. Nowadays most of the popular Python packages provide binaries.
The anaconda/conda-forge distributions also take away the pain of keeping track of underlying non-pythonic libraries (like CUDA, c-libraries in general).
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Dear researchers,
I am trying to fit a FTIR spectrum with a reference spectrum using linear regression. However, I ended up with errors regarding the shape mismatch of the files used. I have tried my best to solve it but I have exhausted the best of my knowledge. I seek your advice on this Python code or how to handle this dataset. Considering the size of the query, I am sharing the Stackoverflow link here.
Any help is highly appreciated.
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Sorry Rahul Suresh , I don't have that much experience with the likelihood formula. But I guess you can calculate the likelihood once you assume which type of distribution you have. You should use the likelihood formula for your type of distribution, not Gaussian if it is not.
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Forecasting using ANN for a single variable. Say, inflation.
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Yes, it is entirely possible to use Artificial Neural Networks (ANNs) for making predictions on a solitary univariate variable using Python. ANNs are versatile models that can be applied to a wide range of tasks, including univariate time series forecasting.
Regards
Jogeswar Tripathy
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I am researching on automatic modulation classification (AMC). I used the "RADIOML 2018.01A" dataset to simulate AMC and used the convolutional long-short term deep neural network (CLDNN) method to model the neural network. But now I want to generate the dataset myself in MATLAB.
My question is, do you know a good sources (papers or codes) that have produced a dataset for AMC in MATLAB (or Python)? In fact, have they produced the In-phase and Quadrature components for different modulations (preferably APSK and PSK)?
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Automatic Modulation Classification (AMC) is a technique used in wireless communication systems to identify the type of modulation being used in a received signal. This is important because different modulation schemes encode information in different ways, and a receiver needs to know the modulation type to properly demodulate the signal and extract the data.
Here's a breakdown of AMC:
  • Applications:Cognitive Radio Networks: AMC helps identify unused spectrum bands for efficient communication. Military and Electronic Warfare: Recognizing communication types used by adversaries. Spectrum Monitoring and Regulation: Ensuring proper usage of allocated frequencies.
  • Types of AMC Algorithms:Likelihood-based (LB): These algorithms compare the received signal with pre-defined models of different modulation schemes. Feature-based (FB): These algorithms extract features from the signal (like amplitude variations) and use them to classify the modulation type.
  • Recent Advancements:Deep Learning: Deep learning architectures, especially Convolutional Neural Networks (CNNs), are showing promising results in AMC due to their ability to automatically learn features from the received signal.
Here are some resources for further reading:
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My Awesomest Network, Are amongst of You #Python #programming #language experts? I am sure there are. Could You help me, please?
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yes pls ask question
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Does anyone know the python code to calculate D10, D50 and D90 from %retain of sieves? Thank you.
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import numpy as np
sieve_sizes = np.array(#Data)
percent_retain = np.array(#Data_Percentage)
cumulative_percentage = np.cumsum(percent_retain)
index_d10 = np.argmax(cumulative_percentage >= 10)
index_d50 = np.argmax(cumulative_percentage >= 50)
index_d90 = np.argmax(cumulative_percentageTry >= 90)
# Corresponding sieve sizes
d10 = sieve_sizes[index_d10]
d50 = sieve_sizes[index_d50]
d90 = sieve_sizes[index_d90]
print(f"D10: {d10} µm")
print(f"D50: {d50} µm")
print(f"D90: {d90} µm")
Try this One I hope this is helpful.
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My Awesomest Network, Is it neccessary to import a main library in Python and then import every sublibrary in parallel or is the first operation enough?
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A Python library is a collection of different modules with specialized functions. You don't need to import all modules (if a sublibrary is how you refer to a module).
You can:
- import library (bringing the namespace to your workspace, thus you can call any module with library.module syntax)
- from library import * (import all modules namespaces to your workspace, this could conflict with other functions/modules/methods)
- from library import module (importing only one module, avoiding load unnecessary modules to your workspace)
- from library import module.method.function (you can dig into the library's tree)
Also, you can assign an alias to libraries and modules, such as:
- import library as lib
- from library import module as mod
There are a few cases when you need to call a module even when you load the library that contains it, but it is not common
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I need the link to download ArcGIS and Python for windows
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  1. Esri Website: ArcGIS is offered by Esri. Visit the Esri website for details on obtaining ArcGIS: https://desktop.arcgis.com/en/arcmap/latest/get-started/installation-guide/introduction.htm
  • This site will guide you through a trial or paid subscription depending on your needs.
Python:
  1. Official Website: Download Python from the official Python website: https://www.python.org/downloads/
  • Choose the latest stable version that matches your Windows system (32-bit or 64-bit).
Additional Notes:
  • ArcGIS and Python Installation: During ArcGIS installation, you'll have the option to install Python as well. This might be the simplest approach if you need both.
  • ArcGIS API for Python: If you plan to use Python for scripting or automation within ArcGIS, you'll likely need the ArcGIS API for Python. Refer to the Esri documentation for installation instructions: https://developers.arcgis.com/python/guide/install-and-set-up/
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My Awesomest Network, As You may know, I am during a process of continuous learning and upskilling. Now I attend Data Science course (SQL, Python et cetera) and I have to do some projects. Could You help me With them, please?
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Final project
Final project
Lending Club is a peer-to-peer lending company that connects borrowers with investors through an online platform. It serves people who need personal loans ranging from $1,000 to $40,000. Borrowers receive the full amount of their loan minus an origination fee that is paid to the company. Investors purchase notes secured by personal loans and pay Lending Club a service fee. Lending Club provides data on all loans originated through its platform during specified periods.
For the purposes of this project, data on loans granted through Lending Club from 2007 to 2011 were used. Each loan has information about whether it has finally been repaid (Fully Paid or Charged off in the loan_status column). Your task is to build a classification model that, based on this data, will predict with a certain accuracy whether a potential borrower will repay his debt under the loan. The data set includes a file with a description of all variables and the "FICO Score ranged.pdf" file, which describes in detail the meaning of one of the columns.
The individual stages of analysis required to complete the project and their scoring are presented below:
Data Processing (70 points) – as an experienced Data Scientist, you probably know the individual steps that need to be performed at this stage, so we will not detail them here.
EDA, i.e. extensive data exploration (100 points) Describe the conclusions drawn from each graph, support your hypotheses with statistical tests such as t-test or Chi-square. Additionally, answer the following questions:
How does a FICO score relate to a borrower's likelihood of repaying a loan?
How does credit age relate to the probability of default and whether this risk is independent of or related to FICO score
How does home mortgage status relate to the likelihood of default?
How is annual income related to the probability of default?
How is employment history related to the likelihood of default?
How is the size of the loan requested related to the probability of default?
Feature Engineering – create 20 new variables (60 points)
Modeling (150 points)
Cluster the data (try several methods, at least 3) and check whether there are any borrower segments, use appropriate methods to determine the optimal number of clusters (40 points)
Train 5 different models, using a different algorithm for each, and then compare their performance, using the AUROC score as the model quality metric. (50 points)
Check the operation of previously used methods on compressed data using PCA, compare the results (AUROC score) with the models trained in the previous section. (20 points)
Build the final model whose AUROC score will be >= 80%, remember to select important variables, cross-validate and tune model parameters, also think about balancing classes. (40 points)
There are 380 points up for grabs in total. A minimum of 300 points is required to pass the project.
Good luck!
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I am wondering if there is any way to refresh the input data from a dynamic text file in COMSOL for each iteration.
I have attempted to do this in Python, but COMSOL only solves the equation for the first input text file and not for any new files generated. The reason for this is that I have coupled COMSOL with a DEM-based software which feeds the input to COMSOL for each iteration. (same situation for the output to save the results as a text file)
While the connection is established through Python codes, I am unsure if Python can trigger the refresh button for each iteration!!!
Any suggestions would be greatly appreciated.
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Achal Singh
Hello,
In my experience, COMSOL performed efficiently during each time step. However, attempting to accelerate the calculation time of your COMSOL model solely through Python scripting using the mph library may face constraints, particularly if the bottleneck stems from the model's complexity or the available computational resources. However, there are several strategies you can consider to optimize the performance:
1. Model Simplification: Simplify your COMSOL model by reducing the number of elements, adjusting mesh refinement settings, or simplifying physics assumptions while ensuring that the essential features of your fluid dynamics problem are retained.
2. Parallel Computing: Utilize parallel computing techniques to distribute the computational workload across multiple CPU cores or nodes. COMSOL Multiphysics supports parallel computing, and you can explore options for parallelizing your simulations within the COMSOL environment or using Python parallel processing libraries like multiprocessing.
3. Solver Settings Optimization: Fine-tune the solver settings within your COMSOL model to achieve better convergence and reduced solution time. Experiment with different solver types, preconditioners, and convergence criteria to find the optimal configuration for your specific problem.
4. Adaptive Mesh Refinement: Implement adaptive mesh refinement techniques to dynamically adjust the mesh density based on solution characteristics, focusing computational resources on regions of interest within the domain.
5. Parameter Optimization: If your simulations involve parameter sweeps or optimization studies, consider using optimization algorithms available within COMSOL or integrating external optimization libraries with Python to efficiently explore the parameter space and identify optimal solutions.
6. Model Order Reduction: Investigate techniques for model order reduction to reduce the computational complexity of your fluid dynamics model while preserving key system dynamics. Techniques such as proper orthogonal decomposition (POD) or reduced basis methods can be effective in achieving significant speedup while maintaining accuracy.
7. GPU Acceleration: Explore the possibility of leveraging GPU acceleration for certain computations within your COMSOL model, as GPUs can offer significant speedup for certain types of numerical calculations compared to traditional CPU-based computations.
8. Profiling and Benchmarking: Use profiling tools to identify computational bottlenecks and areas for optimization within your COMSOL model. Benchmark different configurations and optimization strategies to quantify the performance improvements achieved and guide further optimization efforts.
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My Awesomest Network, Could You recommend me the best #Python on - line editor with all frameworks and libraries, please?
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google collab
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I'm trying to solve the integral shown in the picture.
I'm using python libraries to plot the integrand (numpy and matplotlib.pyplot), as well as scipy.integrate library to solve the integral.
However, I'd like to see other suggestions or tips to solve this problem.
Any comment will be well appreciated.
Thanks, Pablo
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I need to perform uncertainty quantification by Monte Carlo Method, using Python in Abaqus, of the laminate grades (ply angle) and variation of the amount of fiber and resin. What recommendation would you give me to start, thank you very much.
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To perform uncertainty quantification using the Monte Carlo Method in Abaqus with Python, you can follow these general steps:
  1. Define the Model: Set up your finite element model in Abaqus for the laminate structure you want to analyze. Define the geometry, material properties, boundary conditions, and loading conditions.
  2. Create Python Scripts: Write Python scripts to automate the process of running simulations and analyzing results. Use the Abaqus scripting interface (Abaqus Scripting Reference Manual) to interact with the Abaqus model and perform operations such as creating instances, assigning materials, applying loads, and running simulations.
  3. Define Parameters for Uncertainty: Identify the parameters that introduce uncertainty in your analysis. This may include variations in ply angle, fiber and resin content, material properties, environmental conditions, etc.
  4. Implement Monte Carlo Simulation: Use Python to generate random samples for the uncertain parameters based on probability distributions. For each sample, modify the Abaqus model accordingly and perform a simulation. Repeat this process for a large number of samples (iterations) to generate a statistically significant dataset.
  5. Analyze Results: Post-process the simulation results to extract relevant quantities of interest (QoI) such as stress, strain, displacement, or failure criteria. Calculate statistical quantities such as mean, standard deviation, probability density functions (PDFs), and cumulative distribution functions (CDFs) for the QoI.
  6. Visualize Results: Visualize the results using plots, histograms, scatter plots, and other graphical representations to gain insights into the variability and uncertainty in the system behavior.
  7. Validate and Interpret Results: Validate the uncertainty quantification results against experimental data or other benchmark models. Interpret the results to understand the impact of uncertainty on the performance and reliability of the laminate structure.
Here are some specific recommendations to get started:
  • Familiarize yourself with Python scripting in Abaqus by referring to the Abaqus Scripting Reference Manual and other documentation available from Dassault Systèmes.
  • Use Python libraries such as NumPy and SciPy for random number generation, probability distributions, and statistical analysis.
  • Consider using the abqscript module in Abaqus to execute Python scripts directly within the Abaqus environment.
  • Break down your analysis into smaller, manageable steps and gradually build up the complexity of your Python scripts as you gain experience.
By following these steps and leveraging Python scripting capabilities in Abaqus, you can perform uncertainty quantification using the Monte Carlo Method for your laminate structure analysis.
Please follow me if it's helpful. All the very best. Regards, Safiul
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AquaCrop-OSPy is a python package to automate tasks from AquaCrop (FAO) via Python. I would like to write some code so that AquaCrop-OSPy can suggest the irrigation schedule. I followed this tutorial regarding the Aqua Crop GUI. (https://www.youtube.com/watch?v=o5P35ogKDvw&ab_channel=FoodandAgricultureOrganizationoftheUnitedNations)
Based on the documentation and some jupyter notebooks, I selected rrMethod=1: Irrigation is triggered if soil water content drops below a specified threshold (or four thresholds representing four major crop growth stages (emergence, canopy growth, max canopy, senescence). I have written the following code (code regarding importing the packages has been removed to keep the question short)
smts = [99]*4 # soil moisture targets [99, 99, 99, 99]
max_irr_season = 300 # 300 mm (water)
path = get_filepath('champion_climate.txt')
wdf = prepare_weather(path)
year1 = 2018
year2 = 2018
maize = Crop('Maize',planting_date='05/01') # define crop
loam = Soil('ClayLoam') # define soil
init_wc = InitialWaterContent(wc_type='Pct',value=[40]) # define initial soil water conditions
irrmngt = IrrigationManagement(irrigation_method=1,SMT=smts,MaxIrrSeason=max_irr_season) # define irrigation management
model = AquaCropModel(f'{year1}/05/01',f'{year2}/10/31',wdf,loam,maize,
irrigation_management=irrmngt,initial_water_content=init_wc)
model.run_model(till_termination=True)
The code runs but I cannot find when and how much water (depth in mm) is irrigitated. model.irrigation_management.Schedule retrurns an array of zeros. The total amount of water is 300mm as can be seen on the code. I also tried dir(model.irrigation_management) to have a look at other methods and attributes but without any success.
Is what I am asking possible via AquaCrop-OSPy or have I misunderstood any concept?
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  1. Install AquaCrop-OSPy: First, you need to install AquaCrop-OSPy on your system. You can find installation instructions in the AquaCrop-OSPy documentation or README file.
  2. Prepare Input Data: Prepare input data required for AquaCrop-OSPy simulation. This includes climate data, soil data, crop data, management data, etc.
  3. Run AquaCrop-OSPy Simulation: Run the AquaCrop-OSPy simulation using the prepared input data. This will simulate crop growth and water use under the given conditions.
  4. Generate Irrigation Schedule: Once the simulation is complete, you can generate the irrigation schedule using the simulation output. AquaCrop-OSPy provides functions to generate irrigation schedules based on the simulated crop water requirements and available water.
# Import necessary modules
import os
from AquaCrop_OSPy import RunAquaCrop
# Set input and output directories
input_dir = 'input_data'
output_dir = 'output_data'
# Run AquaCrop-OSPy simulation
RunAquaCrop(input_dir, output_dir)
# Generate irrigation schedule
irrigation_schedule = generate_irrigation_schedule(output_dir)
# Save irrigation schedule to a file
output_file = os.path.join(output_dir, 'irrigation_schedule.csv')
irrigation_schedule.to_csv(output_file)
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Hi everyone, I am using Autodock and I'm fairly new and unskilled in it. I was performing a protein-ligand dock. I prepared the protein and ligand, saved them in pdbqt, prepared the gpf file and set the autogrind.exe and parameter file for running autogrid. But when I click on launch, it doesnt generate the glg and map files.
I'm not sure if this is of context but when I choose my ligand to set map types, it shows me a warning and a python shell errow, both of which I have attached below,
What should I do? Can anyone help me?
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I'm pretty sure the ussue is not with the protein since I've been using this protein for other docking projects too, and didn't face this issue. I was successfully able to generate a glg and a dlg file both. Therefore I think the issue lies in the ligand. But I downloaded the ligand structure directly from pubchem so I hardly think there's any structural there too.
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Dear all,
The overall goal is to disaggregate RCM output from daily resolution to 15 min resolution for different stations. For the stations, I have time series of about 10 years with 15 min resolutions for "calibration". Any suggestions on suitable approaches ...? I would be happy if the code (matlab, python) can be distributed. In the optimal case, several methods will be tested and compared w.r.t. their performance to represent 15 min resolution.
Cheers, Patrick
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Thank you. I will check in due time.
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Help me fix error "modulenotfounderror: no module named 'keras'". Python: 3.11.7; Tensorflow: 2.15.0; Keras: 2.15.0. Update both of them on the latest version but cannot work.
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Thank you for your help. I asked AI, it said Keras only supports 3.9 and below, not yet supporting Python 3.12. So I reinstalled python 3.9 and the error was resolved
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write the normal code for the Simple Algorithm for Yield Estimation (SAFY) in python for Data simulation
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Please find the (commented) code here:
```
import numpy as np
def safy_simulation(num_samples, true_yield_mean, true_yield_std, measurement_error_std): # Generate true yield values
true_yield = np.random.normal(true_yield_mean, true_yield_std, num_samples) # Simulate measurement error
measurement_error = np.random.normal(0, measurement_error_std, num_samples) # Simulate measured yield by adding measurement error to true yield
measured_yield = true_yield + measurement_error
return true_yield, measured_yield
# Example usage, this is for you to change:
num_samples = 2000
true_yield_mean = 50
true_yield_std = 5
measurement_error_std = 2
true_yield, measured_yield = safy_simulation(num_samples, true_yield_mean, true_yield_std, measurement_error_std)
# Print a few samples
for i in range(5):
print(f"Sample {i + 1}: True Yield = {true_yield[i]:.2f}, Measured Yield = {measured_yield[i]:.2f}")
```
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Hello, I'm doing research on the degree of optimization of a groundwater monitoring network for a study area in The Netherlands. I'm conducting an elimination approach; monitoring wells that do not have informational relevance to the network are eliminated from the network. Now, I would like to analyze the sensitivity of the input data (groundwater level data of all monitoring wells) to understand how variations in the input data can affect the output of the model (optimal number of monitoring wells, monitoring wells that area eliminated). The sensitivity analysis would give insight into the reliability of the model, thinking of the eliminated monitoring wells and how I can minimize the RMSE of the model and MAE of the eliminated monitoring wells. What would be a suitable method for a SA in Python? I heard things about Monte Carlo and Sobol, but I'm not sure if those will fit in my Python script.
Many thanks in advance!
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Dear Engr. Tufail , many thanks for your detailed answer and suggestions to my query!
If I understand it correctly, it is the best to provide different scenarios (high and low GWL data e.g.), compare the results of each scenario, and evaluate the results of the scenario by analyzing the RMSE of the reduction percentage and the MAE of the eliminated monitoring wells.
Do you also have a suggestion on an approach to determine the ideal reduction percentage for elimination? This is in correlation with the RMSE. A result of the elimination will be: a figure which describes: x-axis: n monitoring wells, y-axis: RMSE, according to the reduction percentage).
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Dear Scientists and Researchers,
I'm thrilled to highlight a significant update from PeptiCloud: new no-code data analysis capabilities specifically designed for researchers. Now, at www.pepticloud.com, you can leverage these powerful tools to enhance your research without the need for coding expertise.
Key Features:
PeptiCloud's latest update lets you:
  • Create Plots: Easily visualize your data for insightful analysis.
  • Conduct Numerical Analysis: Analyze datasets with precision, no coding required.
  • Utilize Advanced Models: Access regression models (linear, polynomial, logistic, lasso, ridge) and machine learning algorithms (KNN and SVM) through a straightforward interface.
The Impact:
This innovation aims to remove the technological hurdles of data analysis, enabling researchers to concentrate on their scientific discoveries. By minimizing the need for programming skills, PeptiCloud is paving the way for more accessible and efficient bioinformatics research.
Join the Conversation:
  1. How do you envision no-code data analysis transforming your research?
  2. Are there any other no-code features you would like to see on PeptiCloud?
  3. If you've used no-code platforms before, how have they impacted your research productivity?
PeptiCloud is dedicated to empowering the bioinformatics community. Your insights and feedback are invaluable to us as we strive to enhance our platform. Visit us at www.pepticloud.com to explore these new features, and don't hesitate to reach out at [email protected] with your thoughts, suggestions, or questions.
Together, let's embark on a journey towards more accessible and impactful research.
Warm regards,
Chris Lee
Bioinformatics Advocate & PeptiCloud Founder
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I think they remove the need for programming skills and make data analysis much easier to do quickly and efficiently! For the future, I look forward to considering adding more no-code functions to meet a wider range of research needs. Just like the no-code platforms used before, a lot of time will be spent on data processing and analysis, and with no-code tools It will make our work easier and easier
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I want to draw cassini oval parametrically with using analytical face option of cst.
I write python code below. If any one can help me ı will really appreciate.
import numpy as np
import matplotlib.pyplot as plt
def cassini_oval(x, y, x1, y1, x2, y2, a):
# Compute the Cassini oval equation
return np.sqrt((y - y1)**2 + (x - x1)**2) * np.sqrt((y - y2)**2 + (x - x2)**2) - a
# Parameters
x1 = -15.0 # x-coordinate of the first focus
y1 = 0.0 # y-coordinate of the first focus
x2 = -x1  # x-coordinate of the second focus
y2 = 0.0 # y-coordinate of the second focus
a = x1**2 # constant 'a' in the equation
# Generate points for plotting
x_range = np.linspace(-30, 30, 1000)
y_range = np.linspace(-30, 30, 1000)
X, Y = np.meshgrid(x_range, y_range)
Z = cassini_oval(X, Y, x1, y1, x2, y2, a)
# Plot Cassini oval
plt.figure()
plt.contour(X, Y, Z, levels=[0], colors='b')
plt.xlabel('x')
plt.ylabel('y')
plt.title('Cassini Oval')
plt.axis('equal')
plt.grid(True)
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Aparna Sathya Murthy thx for your answer but ı already have equations but dont know how can ı insert in CST ? Because CST want X and Y fuctions seperatly to calculate and doesnt accept the equation form allowing us to enter functions. But ı must enter the Zero as a result or R as a radius
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It is possible here that we suggest new topics that are suitable as research, master’s theses, or doctoral dissertations on the application of artificial intelligence or programming in the Python language on demographic topics or population geography.
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Zainab mohammed Ameen, Artificial intelligence (AI) has become a novel and powerful approach in analyzing population issues and gained the attention of demographers, enhancing the position of population studies in a deeper understanding of population phenomena. Some useful links:
  1. https://www.nature.com/articles/s41746-018-0058-9
  2. https://www.nia.nih.gov/research/milestones/epidemiology-population-studies/population-studies-artificial-intelligence
To conclude, As AI continues to evolve, its impact on demography will become even more profound, leading to improved policy decisions and resource allocation strategies.
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RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable.
res = hypotest_fun_out(*samples, **kwds)
Above warning occured in python. Firstly, the dataset was normalised and then while performing the t-test this warning appeared, though the output was displayed. Kindly suggest some methods to avoid this warning.
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Why do you normalize before testing? If you are doing a pairwise t-test and the differences are small this only makes differences smaller. https://www.stat.umn.edu/geyer/3701/notes/arithmetic.html
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Please I have a question. Can someone help me ? I want to connect NetSim with Python, that's the error message: ConnectionResetError: [WinError 10054] An existing connection was forcibly closed by the remote host
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You could check the knowledgebase https://support.tetcos.com/support/home. In the same link you could also raise a support ticket with the developers who are usually responsive.
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Semi-Supervised Learning in Statistics
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you can deploy logistic regression algorithm for this task
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I want to use Python for coding in NetSim, but the source code provided is only in C language, with some examples in Matlab. From where can I find and learn the same in python?
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Please I have a question. Can someone help me ? I want to connect NetSim with Python, that's the error message: ConnectionResetError: [WinError 10054] An existing connection was forcibly closed by the remote host
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I request to share if you have any code or idea on computation of number of domination sets in a given graph using MATLAB OR PYTHON
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Using greedy algorithm we can find dominating sets for a graph
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Can someone help me with the PYTHON code for this Self-Exciting Threshold Autoregressive model (SETAR)?
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pip install setar
import numpy as np
import setar
# Generate some sample data
np.random.seed(0)
n = 200
x = np.random.randn(n)
# Introduce a threshold at index 100
x[100:] += 1
# Fit a SETAR model
model = setar.SETAR(x, p=2, d=0, q=0, k=1)
# Print the estimated threshold and coefficients
print("Estimated Threshold:", model.threshold)
print("Estimated Coefficients:", model.coeffs)
Use this in ayny Python Enviroment
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Hi there, I am having an issue delineating the watershed. I am trying to load a .tif file and when I click 'create streams' I get the following error (attached). It's not a problem with QSwat+ software because I was able to follow tutorials online using the software, without issue. Any help would be greatly appreciated.
Edit: the error reads as follows:
*** Problem with TauDEM /Users/user/SWATPlus/TauDEM5Bin/pitremove -z /Users/user/Documents/Masters/Swat+/CGD Pre Harvest/Preharvest5/Preharvest/Watershed/Rasters/DEM/DEM_IRL_ITM.tif -fel /Users/user/Documents/Masters/Swat+/CGD Pre Harvest/Preharvest5/Preharvest/Watershed/Rasters/DEM/DEM_IRL_ITMfel.tif: please examine output above. ***
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Dear Eibhlín Vaughan,
To further diagnose if the issue is with SWAT+ or TauDEM, try running the TauDEM pitremove operation independently outside of SWAT+ using the same input DEM file. This can determine if the issue arises from interaction with SWAT+ or is inherent to TauDEM. Also verify the input DEM raster format is supported by TauDEM, as some formats like GeoTIFF typically work better than others. Start with a very small 10m x 10m subset of the DEM to see if pitremove succeeds on that, then progressively increase the area size to isolate any problems related to data complexity or resource demands. If memory or performance seem insufficient, try decreasing the resolution or computational resources allocated to pitremove. Taking these steps to narrow down the root of the problem can clarify whether the pitremove failure stems from SWAT+ linkage or limitations within TauDEM itself.
Humble Regards,
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I have daily water level data for a river and the Reduced Level (RL) values for the cross-section as the y axis at every 3 m of the cross-section. How do I write a python program to calculate the cross-sectional area for daily water level where the water level data is to be taken automatically from the excel or CSV file. If anyone has done this type of thing, please help me.
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Hi,
I have same task now, have you find any answer?
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#ComputerScience, #Python, #MATLAB, #AI, #AIML, #ML, #Research, #Medical, #HearDisease.
Inviting serious researchers into heart disease prediction before it reaches its peak level.
It has been found in various research papers that patients reach the hospital when the disease has reached its peak level; consulting doctors and experts before disease maturity is an advantage.
There are various technologies that can be discussed, including basic training, ideas, and problem-solving topics.
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According to this study, the Random Forest technique has produced the best results, with an accuracy rate of 90% compared to other machine learning methods. The use of machine-learning methods, such as logistic regression and K-NN, to predict and categorize patients with heart disease is recommended by Jindal et al.
Regards,
Shafagat
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PARODY
In the New Yorker, Wolcott Gibbs wrote that parody is the hardest form of creative writing because the style of the subject must be reproduced in slightly enlarged form, while at the same time holding the interest of people who haven’t read the original. Further complications are posed since it must entertain at the same time that it criticizes and must be written in a style that is not the writer’s own. He concluded that the only thing that would make it more difficult would be to write it in Cantonese.
Obviously, it is easier for people to enjoy a parody if they know what the original was. In our increasingly diverse culture, memories of “classic” children’s books may be one of the few things we have in common. Advertisers, broadcasters, cartoonists, journalists, politicians, bloggers, and everyone else who wants to communicate with large numbers of people, therefore turn to the array of exaggerated characters that we remember from childhood books. Chicken Little represented alarmists; Pinocchio stood for liars; The Big Bad Wolf warned us of danger; Humpty Dumpty demonstrated how easy it is to fall from grace; The Frog Prince gave hope to women of all ages; and Judith Viorst’s The Terrible, Horrible, No Good, Very Bad Day lets us know that we all have really bad days.
Some of Lewis Carroll’s parodies were just for fun. When Lewis Carroll wrote a parody of the poem “Twinkle Twinkle, Little Star. How I wonder where you are,” it became, “Twinkle Twinkle, Little Bat. How I wonder where you’re at.” This is merely fun word play. But some of Carroll’s parodies had a deeper significance. Lewis Carroll lived in a time when the Victorian poetry tended to be filled with sentimentality and didacticism, so many of Carroll’s poems parodied that sentimentality and didacticism. G. W. Langford wrote a poem that not only preached to parents, but also reminded them of the high mortality rate for young children: “Speak gently to the little child! / It’s love be sure to gain; / Teach it in accents soft and mild; It may not long remain.” Carroll’s parody turned this poem into a song for the Duchess to sing to a piglet wrapped in baby clothes: “Speak roughly to your little boy. And beat him when he sneezes. / He only does it to annoy / Because he knows it teases.” The poem “Against Idleness and Mischief” by Isaac Watts read as follows: “How doth the little busy bee / Improve each shining hour / and gather honey all the day / From every opening flower!” Lewis Carroll’s parody is much more fun, and much less didactic: “How doth the little crocodile / Improve his shining tail / And pour the waters of the Nile / On every golden scale?”
Each of the adventures in Jonathan Swift’s Gulliver’s Travels is a satirical parody of exploration and expansion, but each is also a parody of British society and politics, especially the British society and politics that were in effect during Swift’s life time. Swift’s “A Modest Proposal for Preventing the Children of Ireland from being a Burden to their Parents or Country” was carefully structured to read like a proposal that would be seriously placed before the British House of Commons, and the various aspects of his proposal were in fact very similar to proposals that were at the time being placed before Parliament. Similarly, Mark Twain’s “War Prayer” had not only the form of a real prayer, but contained many of the expressions and clichés that could be found in prayers of the day. The “War Prayer” begins “Oh Lord our God, help us to tear their soldiers to bloody shreds with our shells…. Lord, blast their hopes, blight their lives, protract their bitter pilgrimage, and make heavy their steps,” and ends “We ask it in the spirit of love, of Him Who is the Source of Love, and Who is the ever-faithful refuge and friend of all that are sore beset and seek his aid. Amen.”
The reason that Edgar Alan Poe is so often parodied is that his poetic style is so distinct. Poe wrote a poem entitled “Bells” which reads as follows: “Hear the sledges with the bells— / Silver bells! / What a world of merriment their melody foretells! / How they tinkle, tinkle, tinkle, / In the Icy air of night! / While the stars that oversprinkle / All the heavens, seem to twinkle / With a crystalline delight….” An anonymous writer wrote the following parody of Poe’s “Bells”: “Hear the fluter with his flute, / Silver flute! / Oh, what a world of wailing is awakened by its toot! / How it demi-semi quavers / On the maddened air of night! / And defieth all endeavors / To escape the sound or sight / Of the flute, flute, flute, With its tootle, tootle, toot… / Of the flute, flewt, fluit, floot, Phlute, Phlewt, Phlewght, / And the tootle, tootle, tooting of its toot.” Poe’s “The Raven” is also often parodied, as is his “Annabel Lee.”
Some authors like Mel Brooks specialize in writing movie-script parodies. Brooks wrote “Blazing Saddles,” “Robin Hood, Men in Tights,” “Young Frankenstein,” and “The Producers.” The plot line of “The Producers” is that the producers heavily insure a play that they are sure will be a flop—but it is so bad that it is a great hit. One of the funniest scenes is when all of the various “Hitlers” are auditioning for the part with their stiff-legged marches, their Hitler mustaches, and their “Heil Hitler” salutes. Who says that there is a subject that is so horrific that it can’t be parodied and satirized? The Monty Python parodies are equally edgy. That group wrote and starred in “The Holy Grail,” “Meaning of Life,” and “The Life of Brian.” The final scene of this last movie shows Brian being crucified, and all of the people being crucified on all of their crosses are singing “Always think of the bright…side…of life. / Ta da, Ta da da da da da.”
Today we are surrounded by parodies, like Quentin Tarentino’s film Pulp Fiction, and Jeffrey Katzenberg’s Shrek, not to mention the “Scary” the “Airplane” movies, and all the rest. And then, there are fake news sources like Mad Magazine, National Lampoon, Harvard Lampoon, The Onion, Real Time with Bill Maher, The Colbert Report, and Jon Stewart’s “The Daily Show.” One humorist quipped “I get my news from “The Daily Show” and my humor from “Fox News.”
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Ghadah: "Who's afraid of Virginia Wolf." Powerful metaphor.
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PARODY
In the New Yorker, Wolcott Gibbs wrote that parody is the hardest form of creative writing because the style of the subject must be reproduced in slightly enlarged form, while at the same time holding the interest of people who haven’t read the original. Further complications are posed since it must entertain at the same time that it criticizes and must be written in a style that is not the writer’s own. He concluded that the only thing that would make it more difficult would be to write it in Cantonese.
Obviously, it is easier for people to enjoy a parody if they know what the original was. In our increasingly diverse culture, memories of “classic” children’s books may be one of the few things we have in common. Advertisers, broadcasters, cartoonists, journalists, politicians, bloggers, and everyone else who wants to communicate with large numbers of people, therefore turn to the array of exaggerated characters that we remember from childhood books. Chicken Little represented alarmists; Pinocchio stood for liars; The Big Bad Wolf warned us of danger; Humpty Dumpty demonstrated how easy it is to fall from grace; The Frog Prince gave hope to women of all ages; and Judith Viorst’s The Terrible, Horrible, No Good, Very Bad Day lets us know that we all have really bad days.
Some of Lewis Carroll’s parodies were just for fun. When Lewis Carroll wrote a parody of the poem “Twinkle Twinkle, Little Star. How I wonder where you are,” it became, “Twinkle Twinkle, Little Bat. How I wonder where you’re at.” This is merely fun word play. But some of Carroll’s parodies had a deeper significance. Lewis Carroll lived in a time when the Victorian poetry tended to be filled with sentimentality and didacticism, so many of Carroll’s poems parodied that sentimentality and didacticism. G. W. Langford wrote a poem that not only preached to parents, but also reminded them of the high mortality rate for young children: “Speak gently to the little child! / It’s love be sure to gain; / Teach it in accents soft and mild; It may not long remain.” Carroll’s parody turned this poem into a song for the Duchess to sing to a piglet wrapped in baby clothes: “Speak roughly to your little boy. And beat him when he sneezes. / He only does it to annoy / Because he knows it teases.” The poem “Against Idleness and Mischief” by Isaac Watts read as follows: “How doth the little busy bee / Improve each shining hour / and gather honey all the day / From every opening flower!” Lewis Carroll’s parody is much more fun, and much less didactic: “How doth the little crocodile / Improve his shining tail / And pour the waters of the Nile / On every golden scale?”
Each of the adventures in Jonathan Swift’s Gulliver’s Travels is a satirical parody of exploration and expansion, but each is also a parody of British society and politics, especially the British society and politics that were in effect during Swift’s life time. Swift’s “A Modest Proposal for Preventing the Children of Ireland from being a Burden to their Parents or Country” was carefully structured to read like a proposal that would be seriously placed before the British House of Commons, and the various aspects of his proposal were in fact very similar to proposals that were at the time being placed before Parliament. Similarly, Mark Twain’s “War Prayer” had not only the form of a real prayer, but contained many of the expressions and clichés that could be found in prayers of the day. The “War Prayer” begins “Oh Lord our God, help us to tear their soldiers to bloody shreds with our shells…. Lord, blast their hopes, blight their lives, protract their bitter pilgrimage, and make heavy their steps,” and ends “We ask it in the spirit of love, of Him Who is the Source of Love, and Who is the ever-faithful refuge and friend of all that are sore beset and seek his aid. Amen.”
The reason that Edgar Alan Poe is so often parodied is that his poetic style is so distinct. Poe wrote a poem entitled “Bells” which reads as follows: “Hear the sledges with the bells— / Silver bells! / What a world of merriment their melody foretells! / How they tinkle, tinkle, tinkle, / In the Icy air of night! / While the stars that oversprinkle / All the heavens, seem to twinkle / With a crystalline delight….” An anonymous writer wrote the following parody of Poe’s “Bells”: “Hear the fluter with his flute, / Silver flute! / Oh, what a world of wailing is awakened by its toot! / How it demi-semi quavers / On the maddened air of night! / And defieth all endeavors / To escape the sound or sight / Of the flute, flute, flute, With its tootle, tootle, toot… / Of the flute, flewt, fluit, floot, Phlute, Phlewt, Phlewght, / And the tootle, tootle, tooting of its toot.” Poe’s “The Raven” is also often parodied, as is his “Annabel Lee.”
Some authors like Mel Brooks specialize in writing movie-script parodies. Brooks wrote “Blazing Saddles,” “Robin Hood, Men in Tights,” “Young Frankenstein,” and “The Producers.” The plot line of “The Producers” is that the producers heavily insure a play that they are sure will be a flop—but it is so bad that it is a great hit. One of the funniest scenes is when all of the various “Hitlers” are auditioning for the part with their stiff-legged marches, their Hitler mustaches, and their “Heil Hitler” salutes. Who says that there is a subject that is so horrific that it can’t be parodied and satirized? The Monty Python parodies are equally edgy. That group wrote and starred in “The Holy Grail,” “Meaning of Life,” and “The Life of Brian.” The final scene of this last movie shows Brian being crucified, and all of the people being crucified on all of their crosses are singing “Always think of the bright…side…of life. / Ta da, Ta da da da da da.”
Today we are surrounded by parodies, like Quentin Tarentino’s film Pulp Fiction, and Jeffrey Katzenberg’s Shrek, not to mention the “Scary” the “Airplane” movies, and all the rest. And then, there are fake news sources like Mad Magazine, National Lampoon, Harvard Lampoon, The Onion, Real Time with Bill Maher, The Colbert Report, and Jon Stewart’s “The Daily Show.” One humorist quipped “I get my news from “The Daily Show” and my humor from “Fox News.”
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Ghadah: Good point. I agree.
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I wonder if is it possible to adjust the number of lanes or link lengths of a road network in the PTV VISSIM during the simulation process.
For example, if the VISSIM simulation lasts for 24 hours, can the number of lanes change every hour through the COM development?
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In Azerbaijan, in 16 regions, a study was conducted to improve Mobility using simulation on PTV VISSIM. Using this program, you can organize flexible management of traffic flows.
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Hello everyone! I want to learn python programming language for conducting exploratory analysis of the Skytrax reviews about airlines. Can anyone guide me which website or platform is the best for the python learning, as the different platforms have been making it time consuming and complicated to learn it quickly?
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Here is a neat and Free Interactive Python Tutorial:
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I'm looking for a Spine Reconstruction tool identifying vertebra from a CT image pile.
I just need to know where the anterior bodies are, and what are the bodies planes orientations (sup and inf ).
Ideally it should cope with ribs, sternum and pelvis bone artefacts.
Should be able to be mostly effective from T10 to S1 including ageing artefacts like osteophytis.
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Thanks Kamar.
It sounds like a founded pathway.
Did you go through it with an available solution ?
Cheers.
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I'm using autodock vina in Python to dock multiple proteins and ligands, but I'm having trouble setting the docking parameters for each protein. How can I do this in Python? (I have attached my py code which I have done in this I have assumed this parameters same for all proteins)
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By the above code, irrespective of protein size the grid box size will be considered as 20x20x20. End of the vina execution, most of the complex shows binding affinity "0" or much less, as the active site will be out of the grid box range. Better increase the grid box size (SIZE_X,Y,Z) up to 60 or 120 each, depending on the maximum proteins (chains in PDB code) size of each complex, and try to run VINA again. Then you may get binding energy values of maximum protein-ligand complexes (sometimes for all).
However, this will not mimic the experimental structure correctly, since you handling bulk protein-ligand (separately) complexes docking with the common configuration file same time.
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I am trying to train a CNN model in Matlab to predict the mean value of a random vector (the Matlab code named Test_2 is attached). To further clarify, I am generating a random vector with 10 components (using rand function) for 500 times. Correspondingly, the figure of each vector versus 1:10 is plotted and saved separately. Moreover, the mean value of each of the 500 randomly generated vectors are calculated and saved. Thereafter, the saved images are used as the input file (X) for training (70%), validating (15%) and testing (15%) a CNN model which is supposed to predict the mean value of the mentioned random vectors (Y). However, the RMSE of the model becomes too high. In other words, the model is not trained despite changing its options and parameters. I would be grateful if anyone could kindly advise.
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Dear Renjith Vijayakumar Selvarani and Dear Qamar Ul Islam,
Many thanks for your notice.
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Hello everyone! I'm very fresher now, like super fresher. I don't know how to research! Even how can I start researching! But I want to research!!
I have a very little idea about python programming language.
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cool...
You start with basics of python, move on with the applications on python in various domains like data analytics, image processing, natual language processing and so on. work on the basics of any of the interested fields of your choice. you start working on any of the algorithm for a specific data or data set. go through and understand the algorithm first... they you will get to know how to proceed. what to change, what to modify.
Have patience. it may not happen in a day. Consistent involvement is requirement is required.
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Hi i have estimated an armax model using python sippy library. The estimation gives me two transfer functions H and G. How can I combine them into a single one to predict model output for new input u(t)or to compute unit step response? I thought to somehow derive state space representation maybe...
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André Kummerow In your case, you've estimated two transfer functions, H and G, using the Python SIPPY library. These transfer functions represent different aspects of the ARMAX model:
  1. H: This transfer function typically represents the relation between the output and the noise in the system.
  2. G: This is the transfer function that relates the exogenous input u(t) to the output.
Now, to predict the model output for new inputs or to compute the unit step response, you need to combine these transfer functions. Here's a simple way to understand the combination process:
  1. Conceptual Understanding: Think of the ARMAX model as a system where your input signal u(t) passes through a filter (represented by G) and adds to a noise component (represented by H) to produce the output. In a more technical sense, the output of the system is the sum of the responses from each transfer function to their respective inputs.
  2. Mathematical Approach: To combine H and G, you'd typically use the principle of superposition, which is valid for linear systems like ARMAX. The total output y(t) of the system can be expressed as the sum of the output due to the input u(t) (processed by G) and the output due to the noise (processed by H).
  3. Implementation: In Python, using libraries like SIPPY or control systems libraries, you can simulate this behavior. For a given input u(t), you can simulate the response of G to this input and separately simulate the response of H to the noise input. Adding these two responses gives you the total system output.
  4. State-Space Representation: Converting to a state-space representation can be a good idea if you're comfortable with it. State-space models offer a more general framework for representing linear systems and can be more intuitive for simulation and control purposes. Each transfer function (H and G) can be represented in state-space form, and you can then combine these state-space models appropriately.
  5. Practical Tips: Ensure that the data you use for simulation is well-prepared, and the noise characteristics (for H) are well understood. The accuracy of your predictions heavily relies on the quality of your model and the data.
  6. Advanced Considerations: If you're delving deeper, consider the frequency response of your combined system and its stability. These are crucial for ensuring that your model behaves as expected in various conditions.
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I want to create a surface for all element faces, it can be done manually, but how can I achieve it in a script?
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Heng Wu, I presume the cube is named "Concrete Cube," and the database for the model is called "Model-1." In that case, the following command is expected to be effective for your purpose, having surface named "Outer Surface" :
# Define surface from Mesh
p = mdb.models['Model-1'].parts['Concrete Cube']
s = p.faces
side1Faces = s.getSequenceFromMask(mask=('[#3f ]', ), )
p.Surface(side1Faces=side1Faces, name='Outer Surface')
While the Python script ( Link to demonstration: https://youtu.be/l91wtTDBd6I ) is attached below as well, as the code is as given here:
# Import the necessary libraries
from abaqus import *
from abaqusConstants import *
from caeModules import *
from driverUtils import executeOnCaeStartup
# Define the Cube Dimensions
s = mdb.models['Model-1'].ConstrainedSketch(name='__profile__',
sheetSize=200.0)
g, v, d, c = s.geometry, s.vertices, s.dimensions, s.constraints
s.setPrimaryObject(option=STANDALONE)
s.rectangle(point1=(-25.0, 25.0), point2=(25.0, -25.0))
p = mdb.models['Model-1'].Part(name='Concrete Cube', dimensionality=THREE_D,
type=DEFORMABLE_BODY)
p = mdb.models['Model-1'].parts['Concrete Cube']
p.BaseSolidExtrude(sketch=s, depth=50.0)
s.unsetPrimaryObject()
p = mdb.models['Model-1'].parts['Concrete Cube']
# Assemble Cube
a = mdb.models['Model-1'].rootAssembly
a.DatumCsysByDefault(CARTESIAN)
p = mdb.models['Model-1'].parts['Concrete Cube']
a.Instance(name='Concrete Cube-1', part=p, dependent=ON)
# Mesh the Cube
p = mdb.models['Model-1'].parts['Concrete Cube']
p.seedPart(size=5.0, deviationFactor=0.1, minSizeFactor=0.1)
p = mdb.models['Model-1'].parts['Concrete Cube']
p.generateMesh()
# Define surface from Mesh
p = mdb.models['Model-1'].parts['Concrete Cube']
s = p.faces
side1Faces = s.getSequenceFromMask(mask=('[#3f ]', ), )
p.Surface(side1Faces=side1Faces, name='Outer Surface')
I hope it help :)
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Good afternoon,
I am using AutoDock4 and I am trying to do the grid and this erro keeps appearing in the Pynthon Controler: swig/python detected a memory leak of type 'BHtree *', no destructor found.
How can I solve it?
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Olga Lopes Imagine your computer's memory as a limited container, like a water tank. When you run a program like AutoDock4, it uses this memory to store information temporarily. However, sometimes, the program doesn't clean up after itself properly, leaving behind "leaks" in that tank. Over time, these leaks can cause your computer to slow down or even crash.
The error message you mentioned, "'BHtree *', no destructor found," essentially means that AutoDock4 is struggling to clean up after itself when it's done with a specific type of memory called 'BHtree.'
To address this issue, you can follow these steps:
  1. Check for Updates: Ensure that you are using the latest version of AutoDock4. Sometimes, newer versions come with bug fixes and improvements that might resolve memory leak problems.
  2. Review Your Code: If you've made any modifications to the AutoDock4 code, double-check it for any errors or memory management issues. Sometimes, a simple coding mistake can lead to memory leaks.
  3. Limit Your Usage: If you're running multiple instances of AutoDock4 or other memory-intensive programs simultaneously, it can exacerbate memory leaks. Try closing unnecessary applications and running AutoDock4 separately to see if that helps.
  4. Consult the Community: Reach out to the AutoDock4 community or forums for help. Others might have faced the same issue and can provide guidance or solutions specific to your problem.
  5. Consider Alternatives: If the memory leak problem persists, you might want to explore alternative molecular docking software that might be more stable on your system.
Lastly, I want to emphasize that solving such technical issues can be frustrating, but don't give up. Learning from challenges like this is part of the journey in scientific research. Keep your determination high, and you'll find a solution that works for you.
#MemoryLeakError #AutoDock4 #ScientificResearch #ProblemSolving #ComputerScience #MolecularDocking
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I am working with a time series dataset using the `fable` package (R). I have fitted several models (e.g., ARIMA) and generated forecasts. The accuracy calculation is resulting in NaN values, and the warning suggests incomplete out-of-sample data.
I am seeking guidance on how to handle this incomplete out-of-sample data issue and successfully calculate accuracy metrics for my time series forecasts. If anyone has encountered a similar problem or has expertise in time series analysis with R, your insights would be greatly appreciated.
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Dear Sachin. You should review every step in such a computation. For all those fcst evaluation criteria to produce NaN's, you should have NaN's generated in the fcst errors, which is really basic stuff.
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Hi guys!
I am currently in my 4th semester (2nd year ending). Due to my negligence I did not plan my future but I would like at least start now. please help me build my resume for the campus interviews.
I am learning python and Java languages at present. And I know the basics of C language . I was suggested to be familiar to Unix operating system. If you have any suggestions for for what to learn or where to join for any experience please let me know.
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you should first concentrate on your studies first
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Guys, good night. I need to use a comparative genomics tool that demonstrates synteny between three species of a genus. But I would like something more visual. I've already used mauve, I don't want circos as it's too complex for my level of bioinformatics. So I wanted some software recommendations or tools that could be run by Ubuntu programs (perl, python, java), and be easier to use. Thank you if anyone can help.
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I don't know exactly which visualizations you are imagining, but you could take a look at EDGAR.
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Hello,
I am a civil engineering graduate, interested in research on transportation with application of machine learning or deep learning. My skillsets include GIS, Python and transportation modelling. I am open to learn any new skills required. Let's collaborate and work in some interesting research.
Thank you,
Regards,
Subash Gupta
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I am also interested in transportation modelling. I have skills in field of GIS, Autocad Civil 3D, Report Writing, Project Management, and other. Plese let me know if you are interested in collaboration. [email protected]
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I am looking for a pythonic solution of
A solution with Julia is available at
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Hi!
This is roughly the translation of the above Julia code to Python:
------------------------------------------------------------------
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
from datetime import datetime
# Define the curve parameters
n = 200
t = np.linspace(0, 6 * np.pi, n)
def f(t):
return t * np.cos(t)
def g(t):
return t * np.sin(t)
def h(t):
return t
def f1(t):
return np.cos(t) - t * np.sin(t)
def f2(t):
return -2 * np.sin(t) - t * np.cos(t)
def g1(t):
return np.sin(t) + t * np.cos(t)
def g2(t):
return 2 * np.cos(t) - t * np.sin(t)
def h1(t):
return 1
def h2(t):
return 0
x = f(t)
y = g(t)
z = h(t)
# Graphical Parameters
molt = 3.0
limx = [np.min(x) - 1, np.max(x) + 1]
limy = [np.min(y) - 1, np.max(y) + 1]
limz = [np.min(z) - 1, np.max(z) + 2]
cam_height = 30
cam_angle = np.linspace(0, 90, num=len(t))
# Create the animation
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
def update(i):
ax.clear()
ax.plot(x, y, z, label="Curve")
draw_trihedron(ax, t[i], i, molt)
ax.set_xlim(limx)
ax.set_ylim(limy)
ax.set_zlim(limz)
ax.view_init(elev=cam_angle[i], azim=0)
print(f"{int(100 * i / len(t))}% -> ")
def draw_trihedron(ax, t, i, molt):
trihedron_size = molt
trihedron = np.array([[0, 0, 0],
[trihedron_size, 0, 0],
[0, trihedron_size, 0],
[0, 0, trihedron_size]])
R = np.array([[f1(t), g1(t), h1(t)],
[f2(t), g2(t), h2(t)],
[0, 0, 1]])
trihedron_rotated = trihedron.dot(R.T)
ax.plot(trihedron_rotated[:, 0], trihedron_rotated[:, 1], trihedron_rotated[:, 2], color='r')
ani = FuncAnimation(fig, update, frames=len(t), interval=100)
# Save the animation as a GIF
now = datetime.now().strftime("%Y-%m-%d_%H:%M:%S")
ani.save(f"{now}.gif", writer='imagemagick', fps=15)
print("END!")
------------------------------------------------------------------
You need to install numpy and matplotlib to run the above code:
pip install matplotlib numpy
Also you may need imagemagick or ffmpeg:
sudo apt-get install imagemagick
sudo apt-get install ffmpeg
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Seeking insights on the most effective Python libraries for visualizing data.
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It's dependent on your output data and number of variables.
but most popular libraries in python for visualization is:
1.matplotlib
2.seaborn
3.plotly
4.bokeh
5.ggplot
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Python, Matlab, Power system optimisation
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Attached steps to install python, after that install the Visual Studio Code, the environment is very similar with Matlab.
Regards Francisco
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Hello
I am trying to calculate the saturation magnetization of CoNiFe at certain temperature and composition and I am using TC-Python to get the data of effective bohr magneton number of the alloy. However, I am not sure if I am doing correctly. I used the code below to do that but I got very high numbers like 50-60. I was expecting around 2.5(max) and 0(min). Could you please help me?
Bohr_magneton = calc_result.get_value_of("BM")
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I noticed that I made a mistake. BM is molar mass of the system. It should be BMAGN but I couldn't get the data so the problem still exists.
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Hello! I hope you are doing well I am currently pursuing an understanding of COGNITIVE RADIO. I want to simulate spectrum sensing. Please, I would appreciate it if you sent matlab or python codes for spectrum sensing in cognitive radio or any useful information on that.
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Just write the name of the methods in github. Ex OMP CoSaMP lasso BP...
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I have a student-teacher network for a self-supervised learning network. Basically, my teacher network predicts classes and calculates the loss and updates its parameters using the gradient flow. Typically, the student network updates its parameters using the moving average of teacher network. But in my case, i have some unique layers for the student network that are needed to train using gradient flow. For instance, as the figure shows, there is a unique layer (layer X) in the student network, and rest are common for both networks. The layer 1 layer 2 and layer 3 in the student network need to be updated with the moving average of teacher network and the layer x needs to be updated with gradient flow. How do I design such a network using Python torch DDP.
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Mohammad Imam Thank you very much for your descriptive answer. what happens if I don't have any specific loss value to be calculated at layer x? Can I update the layer x weights with the teacher network loss?
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Hi, I used material studio and biuld selnium nanoparticle. I used autodock and dock nanoparticle with hsa . when input ligand I recieved this error.
Python 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)] on win32
Type "copyright", "credits" or "license()" for more information.
****************************************************************
Personal firewall software may warn about the connection IDLE
makes to its subprocess using this computer's internal loopback
interface. This connection is not visible on any external
interface and no data is sent to or received from the Internet.
****************************************************************
IDLE 1.2.2 ==== No Subprocess ====
>>> adding gasteiger charges to receptor
NanoSe3: :MOL2:Se and NanoSe3: :MOL2:Se have the same coordinates
ERROR *********************************************
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
result = command( *args, **kw )
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1008, in doit
initLPO4(mol, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1019, in __init__
detect_bonds_between_cycles=detect_bonds_between_cycles)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 768, in __init__
delete_single_nonstd_residues=False)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 143, in __init__
self.addCharges(mol, charges_to_add)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 229, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
self.valence_two()
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two
angle1 = bond_angle(k.coords, a.coords, l.coords)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\util.py", line 47, in bond_angle
raise ZeroDivisionError("Input used:", a, b, c)
ZeroDivisionError: ('Input used:', [-3.7719999999999998, -9.9429999999999996, -5.774], [-3.7719999999999998, -9.9429999999999996, -5.774], [-3.7719999999999998, -9.9429999999999996, -5.774])
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Hi tanks a lot. I appreciate that.
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Hello folks, I am trying to install genice2 software.Even after satisfying the per-reqistics and installing completely when i try to run it the error i am getting is " cell: np.ndarray[3, 3] = None,
TypeError: Type subscription requires python >= 3.9"
Can someone tell what to do know? How to resolve this error ?
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Thankyou so much for your reply Mohammad Imam but i have tried everything that you but it is still not working.
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Suppose, we need to solve 1D heat conduction equation numerically to simulate the heat transfer for a steel rod where convection occurs at its surface. Now, how to solve the 1D heat conduction equation considering the convection scenario also as boundary conditions? any suggestion or resources?
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Thanks Professor Filippo Maria Denaro
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Ray is a unified framework for scaling AI and Python applications. Ray consists of a core distributed runtime and a set of AI Libraries for accelerating ML workloads.
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Running Linux ubuntu in windows 11 using WSL
I have anaconda3 installed
I'm running the covalent docking tutorial for autodock vina available from:
When i run the prepareCovalent.py script I get the following:
Input:
(vina) gorrie06@DMGLaptop:~/docking/covalent$ python ~/docking/covalent/adcovalent/prepareCovalent.py --ligand /3upo_test/ligand.mol2 --ligindices 1,2 --receptor /3upo_test/3upo_protein.pdb --residue B:SER222 --outputfile ligcov.pdb
Output:
Traceback (most recent call last):
File "/home/gorrie06/docking/covalent/adcovalent/prepareCovalent.py", line 36, in <module>
import pybel
File "/home/gorrie06/anaconda3/envs/vina/lib/python2.7/site-packages/pybel.py", line 89, in <module>
informats = _formatstodict(_obconv.GetSupportedInputFormat())
File "/home/gorrie06/anaconda3/envs/vina/lib/python2.7/site-packages/pybel.py", line 68, in _formatstodict
broken = [(x, y.strip()) for x, y in broken]
ValueError: need more than 1 value to unpack
This is the function that is being referred to by the output (from pybel.py):
def _formatstodict(list):
if sys.platform[:4] == "java":
list = [list.get(i) for i in range(list.size())]
broken = [x.replace("[Read-only]", "").replace("[Write-only]", "").split(
" -- ") for x in list]
broken = [(x, y.strip()) for x, y in broken]
return dict(broken)
I have been able to modify pybel.py to prevent error but then the script prepareCovalent.py fails to read the pdb file.
Any help is greatly appreciated!
Thank you!
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The error suggests an issue with the `broken` list in the `_formatstodict` function of `pybel.py`.
Try updating the `pybel` package to a compatible version by running the following command in your terminal:
```bash
(vina) gorrie06@DMGLaptop:~/docking/covalent$ pip install --upgrade pybel
```
This command will upgrade the `pybel` package to the latest version available. After upgrading, try running the `prepareCovalent.py` script again to see if the issue is resolved.
If the issue persists or upgrading `pybel` doesn't work, you can try using an alternative approach to run the covalent docking tutorial. Instead of using the `pybel` package, you can use the `rdkit` package, which is a powerful cheminformatics library that can handle various file formats, including PDB files.
To use `rdkit` in your script, you will need to install it by running the following command:
```bash
(vina) gorrie06@DMGLaptop:~/docking/covalent$ pip install rdkit
```
Once `rdkit` is installed, you can modify the `prepareCovalent.py` script to replace the `pybel` import and related code with the corresponding `rdkit` code for reading PDB files. Here's an example of how you can modify the script:
1. Open the `prepareCovalent.py` script in a text editor.
2. Remove the line `import pybel`.
3. Replace the line `ligand = pybel.readfile("mol2", ligandfile).next()` with the following code:
```python
from rdkit import Chem
ligand = Chem.MolFromMol2File(ligandfile)
```
4. Replace the line `receptor = pybel.readfile("pdb", receptorfile).next()` with the following code:
```python
receptor = Chem.MolFromPDBFile(receptorfile)
```
5. Save the modified script.
With these modifications, the script should now use `rdkit` instead of `pybel` for reading the ligand and receptor files. This should resolve the issue you encountered with `pybel` and allow the script to read the PDB file correctly. Make sure you have the `rdkit` package installed in your Anaconda environment (`vina`) before running the modified script.
Good luck: partial credit AI
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I need a sample code for disease modelling optimal control using python program to understand how the code works.
Thank you and God Bless us all
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Basic susceptible-infected-recovered (SIR) model with scipy.optimize module to find the optimal control strategy.
## import needed Python libraries
import numpy as np
from scipy.integrate import odeint
from scipy.optimize import minimize
# Define the SIR model
def sir_model(y, t, beta, gamma, u):
S, I, R = y
dSdt = -beta * S * I + u
dIdt = beta * S * I - gamma * I
dRdt = gamma * I
return [dSdt, dIdt, dRdt]
# Define the objective function to minimize
def objective(u, t, y0, beta, gamma):
y = odeint(sir_model, y0, t, args=(beta, gamma, u))
I = y[:, 1]
return -I[-1] # maximize the final number of infected individuals
# Define the constraints for the control variable
def constraint(u):
return 1 - u # enforce u <= 1
# Set initial conditions and parameters
y0 = [0.99, 0.01, 0.0] # initial values of S, I, R
beta = 0.2 # infection rate
gamma = 0.1 # recovery rate
T = 100 # time horizon
t = np.linspace(0, T, T+1) # time grid
# Perform optimization
u0 = 0.5 # initial guess for the control variable
result = minimize(objective, u0, args=(t, y0, beta, gamma),
constraints={'type': 'ineq', 'fun': constraint, 'jac': lambda x: -1})
# Extract the optimal control strategy
u_opt = result.x
# Simulate the SIR model with the optimal control
y_opt = odeint(sir_model, y0, t, args=(beta, gamma, u_opt))
# Plot the results
import matplotlib.pyplot as plt
plt.plot(t, y_opt[:, 0], label='S')
plt.plot(t, y_opt[:, 1], label='I')
plt.plot(t, y_opt[:, 2], label='R')
plt.xlabel('Time')
plt.ylabel('Population')
plt.legend()
```
SIR model is defined as a set of ordinary differential equations (ODEs) in the `sir_model` function. The objective function `objective` is defined to maximize the final number of infected individuals by adjusting the control variable `u`. The constraint function `constraint` enforces the constraint `u <= 1`. The initial conditions and model parameters are set, and the optimization is performed using the `minimize` function from `scipy.optimize`. The optimal control strategy `u_opt` is extracted from the optimization result, and the SIR model is simulated with this control strategy. Finally, the results are plotted using `matplotlib.pyplot`.
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I want to run python codes on the current variables of Stata using PyStata. For example:
  • set obs 5
  • gen a = _n
  • python
  • a
  • end
But python does not recognize "a". Instead I should run:
  • python
  • a = [1, 2, 3, 4, 5]
  • a
  • end
How can I use the existed "a" instead of new coding?
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Hi there. I want to resample all Sentinel-2 bands to 10 meters. I know snappy has several methods for this, but I was wondering what approaches or packages in python outside of Snappy do you think are the best.
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Few here
1. **Rasterio**: Rasterio is a powerful Python library for reading and writing geospatial raster data. It provides functionality for resampling raster datasets to a desired resolution. You can use the `rasterio.warp.reproject()` function to resample Sentinel-2 bands. Here's an example:
```python
import rasterio
from rasterio.enums import Resampling
# Open the input Sentinel-2 band
with rasterio.open('path/to/input_band.tif') as src:
# Define the desired spatial resolution
dst_resolution = (10, 10) # 10 meters
# Define the output profile
dst_profile = src.profile
dst_profile.update(transform=src.transform,
width=int(src.width * src.transform.a / dst_resolution[0]),
height=int(src.height * src.transform.e / dst_resolution[1]))
# Resample the band
with rasterio.open('path/to/output_band.tif', 'w', **dst_profile) as dst:
rasterio.warp.reproject(source=rasterio.band(src, 1),
src_transform=src.transform,
src_crs=src.crs,
dst_transform=dst.transform,
dst_crs=src.crs,
resampling=Resampling.bilinear)
```
2. **GDAL**: GDAL (Geospatial Data Abstraction Library) is a popular geospatial library that provides extensive capabilities for working with raster data. You can use the GDAL Python bindings to resample Sentinel-2 bands. Here's an example:
```python
from osgeo import gdal
# Open the input Sentinel-2 band
src_dataset = gdal.Open('path/to/input_band.tif')
# Define the desired spatial resolution
dst_resolution = [10, 10] # 10 meters
# Resample the band
gdal.Warp('path/to/output_band.tif',
src_dataset,
xRes=dst_resolution[0],
yRes=dst_resolution[1],
resampleAlg=gdal.GRA_Bilinear)
```
3. **RSGISLib**: RSGISLib is a remote sensing and GIS library that provides various tools for working with raster datasets. It includes resampling functionality that can be used to resample Sentinel-2 bands. Here's an example:
```python
import rsgislib
# Open the input Sentinel-2 band
src_image = rsgislib.imageutils.openImage('path/to/input_band.tif')
# Define the desired spatial resolution
dst_resolution = 10 # 10 meters
# Resample the band
rsgislib.imageutils.resampleImage2Match(src_image,
'path/to/output_band.tif',
'GTiff',
'cubic',
dst_resolution,
dst_resolution)
```
These are a few examples of Python packages
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Hello dear, I request you all please guide me how to resolve this issue.
I dual booted my pc and created the ubuntu and windows as separate OS. Thereafter followed the guidelines and installed the Desmond (Desmond_Maestro_2023.2) in Linux OS but I encountered with the problem.
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
Available platform plugins are: linuxfb, minimal, offscreen, vkkhrdisplay, vnc, xcb.
Fatal Python error: Aborted
I request you all please guide me how to resolve this issue.
Relevant answer
Answer
Here are a few steps you can try to resolve the problem:
1. Verify Qt installation: Make sure that the Qt libraries are properly installed on your Ubuntu system. You can do this by running the following command in the terminal:
````
sudo apt-get install libxcb-xinerama0
```
2. Verify environment variables: Check if the necessary environment variables are set correctly. Specifically, the `LD_LIBRARY_PATH` variable needs to include the path to the Qt libraries. You can check the current value of this variable by running:
````
echo $LD_LIBRARY_PATH
```
If the variable is not set or does not include the path to the Qt libraries, you can add it by editing the `.bashrc` file in your home directory. Open the file using a text editor and add the following line at the end:
````
export LD_LIBRARY_PATH=/path/to/qt/lib:$LD_LIBRARY_PATH
```
Replace `/path/to/qt/lib` with the actual path to the Qt libraries on your system.
3. Reinstall the application: Try reinstalling the Desmond Maestro application. This can help ensure that all necessary files and dependencies are properly installed. Make sure to completely remove the existing installation before reinstalling.
4. Update graphics drivers: Outdated or incompatible graphics drivers can sometimes cause issues with Qt plugins. Try updating your graphics drivers to the latest version available for your system. You can usually do this through the "Additional Drivers" or "Software & Updates" utility in Ubuntu.
5. Try a different Qt platform plugin: If the above steps do not resolve the issue, you can try using a different Qt platform plugin. You can set the `QT_QPA_PLATFORM_PLUGIN_PATH` environment variable to specify a different plugin. For example, you can try using the "minimal" plugin by running the following command before launching the application:
````
export QT_QPA_PLATFORM_PLUGIN_PATH=/path/to/qt/plugins/platforms
```
Replace `/path/to/qt/plugins/platforms` with the actual path to the Qt plugins directory on your system.
If none of the above steps resolve the issue, there may be a compatibility problem between Desmond Maestro and your specific Linux distribution or version.
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How to integrate Cupcarbon and Sumo to implement Iot-aware neurofuzzy-based traffic control system? I am working on the implementation of my research. I need the best approach to do the above . I need the best programming choice python or matlab or java
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Answer
Here's a step-by-step guide but You MUST understand and run simulation at every step
1. Understand the Tools:
CupCarbon is a wireless sensor network simulator, while SUMO is a traffic simulation software.
2. Set up the Environment:
Install CupCarbon and SUMO on your machine, ensuring that they are properly configured and working individually. Make sure you have Python installed as well.
3. Define the System Architecture:
Design the architecture of your IoT-aware neurofuzzy-based traffic control system. Identify the components, interfaces, and data flow between CupCarbon, SUMO, and your neurofuzzy-based traffic control system.
4. Implement the Neurofuzzy-Based Traffic Control System:
Develop the neurofuzzy-based traffic control system using Python. You can use libraries such as scikit-fuzzy or neuro-fuzzy systems to implement the neurofuzzy logic.
5. Interface CupCarbon with Python:
CupCarbon provides a Python API that allows you to control and interact with the simulator programmatically. Use the CupCarbon Python API to create, configure, and control the wireless sensor network in CupCarbon from your Python code.
6. Interface SUMO with Python:
Similarly, SUMO also provides a Python API called "traci" (Traffic Control Interface) that allows you to interact with the SUMO traffic simulation. Use the traci API to control the traffic simulation from your Python code.
7. Establish Communication between CupCarbon and SUMO:
Develop a communication mechanism between CupCarbon and SUMO. You can use sockets or a message queue system to exchange data between the two simulators. For example, CupCarbon can provide sensor information to SUMO, which can then adjust the traffic simulation based on the received data.
8. Integrate the Neurofuzzy-Based Traffic Control System:
Integrate traffic control system with CupCarbon and SUMO. Use the data received from CupCarbon and SUMO to make intelligent decisions in your traffic control system and control the traffic in the simulation accordingly.
9. Test and Evaluate:
Run simulations and evaluate the performance of your integrated system. Collect relevant metrics and analyze the results to assess the effectiveness of your IoT-aware neurofuzzy-based traffic control system.
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I've tried multiple times without success to call my EES code from Python, passing inputs and handling the output. Utilizing the EES Connector from this link (https://pypi.org/project/EES-connector/), I followed the instructions meticulously. Despite successfully applying entries, the issue persists, and the expected values are not returned.
here is the codes I wrote:
======================================
Python code:
------------------------------------------------------
from EESConnect import EESConnector
from tkinter import filedialog
import tkinter as tk
#select the ees file path
root = tk.Tk()
root.withdraw()
ees_file_path = filedialog.askopenfilename()
with EESConnector() as ees:
ees.ees_file_path = ees_file_path
result = ees.calculate(["air_ha", 383, 101.325])
print(result[1])
======================================
EES code:
------------------------------------------------------
$UnitSystem SI K kPa kJ
$Import 'ees_input.dat' file$ F$ T P
h=enthalpy(F$, T=T, P=P)
s=entropy(F$, T=T, P=P)
$Export 'ees_output.dat' file$ h s
======================================
Thank you in advance for your response.
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Sorry, I can not help without knowing your exact environmet
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I want to know how effective this course for researchers with non-computer science background working with thermal engineering problems.
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Without a computer science background will depend on various factors, including the course content, instructor expertise, your commitment to learning, and your ability to apply the knowledge in practical scenarios.
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Hello together,
Transmission and Reflection Free-Space Method have been used to get S-parameters of our MUT. As a next step we used scikit-rf for time-domain analysis and gating.
Is there a free available Python or Matlab algorithm (NRW?) to extract relative permittivity taking into account the Free Space Measurement Method? Thanks in advance.
Relevant answer
Answer
In MATLAB, use the RF Toolbox.
```matlab
% Load your measured S-parameters
sparams = sparameters('path_to_sparams.s2p');
% Extract relative permittivity
epsilon_r = rfparam(sparams, 1, 1, 'EpsilonR');
disp(['Relative permittivity: ' num2str(epsilon_r)]);
```
You need to perform necessary calibration and gating steps on your time-domain data using scikit-rf or other appropriate tools before extracting the relative permittivity. Replace `'path_to_sparams.s2p'` in the code snippets with the actual path to your measured S-parameter file.
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While docking using AutodockTools 1.5.7, this msg pops up in the command prompt while inserting protein, but grid parameter files and the binding affinity results are perfectly generated. Is it ok to continue docking with other ligands while this error(swig/python detected a memory leak of type 'bhtree *', no destructor found) shows up?
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Did you find the solution to solve this problem? I have the same error and try to use another Windows system, but it's useless.
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I have downloaded 5 years daily precipitation data of MSWEP, but i havent succeded in subsetting it for Indonesia region and make pandas dataframe of it using python. Please advise?
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Answer
Follow these steps using Python:
1. Install the necessary libraries:
````
pip install pandas
```
2. Import the required libraries:
````python
import pandas as pd
```
3. Load the data: Assuming you have your MSWEP precipitation data in a CSV file, you can load it into a pandas dataframe using the `read_csv()` function. Provide the path to your CSV file as the argument:
````python
data = pd.read_csv("path/to/your/mswep_data.csv")
```
4. Subset the data for Indonesia: assume you want to subset the data for a latitude range of -11 to 6 and a longitude range of 95 to 141:
````python
indonesia_data = data[(data['latitude'] >= -11) & (data['latitude'] <= 6) & (data['longitude'] >= 95) & (data['longitude'] <= 141)]
```
Replace `'latitude'` and `'longitude'` with the column names that contain the corresponding information in your dataset.
5. Create a pandas dataframe: create a new dataframe with those columns. For example, if you want to keep the date and precipitation columns:
````python
indonesia_df = indonesia_data[['date', 'precipitation']]
```
Replace `'date'` and `'precipitation'` with the column names that represent the date and precipitation values in your dataset.
6. Optional: Save the subsetted dataframe to a new CSV file:
````python
indonesia_df.to_csv("path/to/save/indonesia_precipitation.csv", index=False)
```
This step allows you to save the subsetted data to a new CSV file if you want to use it later.
Hope it helps.
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Mapsim can extract the system equation. I want to develop a tool in Python or MATLAB to automatically derive the system equation for mechanical mechanisms, such as linkage mechanisms. Is there any open source available for reference?
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@Mohammad Imam
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I am using the open-source Python package, pygfunction, to model a BTES system to meet heating demands in a district heating network. Apart from obtaining fluid temperature profiles inside the borehole and inlet/outlet temperatures, I am interested in investigating the development of temperature outside the bore field in the surrounding soil.
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Hi Paul Fleuchaus, unfortunately, I have not been able to dive more into this because of the time crunch of my thesis. But I got the following tips from Dr. Cimmino, who is the creator of pygfunction:
"The package does not directly support the calculation of ground temperatures since they are not useful in the simulation of ground-source heat pump systems.
When g-functions are calculated with the option `'profiles':True`, the g-function object also saves the distribution of loads among the line sources. Theoretically, these could be used as weights for the spatial superposition of the finite line source solution. Then this superimposed solution could be used with load aggregation to follow the temperature variation at a specific coordinate in the ground."
If you are successful with this, I would be highly interested.
Best,
Indrajit
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We have the ECLIPSE executable that we can call, there is an ECLIPSE input text file called input.DATA which includes well location in x and y directions. optimizer should change the x and y locations of the wells each time and then simulations need to be automatically submitted by PYTHON for the specified number of times and gives the field production values each time. we want to maximize the output: Cumulative Oil Production which exists in the output file.
then we will find the best configuration of wells in the field that maximizes the cumulative oil production.
I appreciate your help.
thanks.
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Answer
First create a numpy array of x y location you want to try out, secondly the well location description in the eclipse data file, cut that section and save in a file , call it change.dat. In the main eclipse data file change that portion and write “INCLUDE” then under it put the “change.dat”. This will make eclipse read that well property as an external file via the include statement. Now write a simple python code using freas and fwrite commands that will take the n by 2 numpy array you created earlier. In a for loop, take each row of the n by. 2 array, use open/fwrite commands on the change .dat file so you can be over writing the X and y location in that file. Run close by invoking “ecl XX.dat” where XX.dat is the main of your eclipse data file. Make sure you use the EXCEL and SERPARATE key words in the data file to output the oil/water/gas production rate to compute your NPV. You can use reinforcement learning to solve for the steepest ascent value of this NPV taking into account the discount factor and oil price per barrel and also cost for disposal and water treatment. You can let RL guide this well locations automatically instead of using brute force.at the end the algorithm will converge on the optimum x and y location with the maximised NPV value. Hope this helps.
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,,
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Dear Doctor
"Python provides a huge number of libraries to work on Big Data. You can also work – in terms of developing code – using Python for Big Data much faster than any other programming language. These two aspects are enabling developers worldwide to embrace Python as the language of choice for Big Data projects."
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Dear all,
thank you for considering this question. Do you know any reason why Daubechies wavelet can't be used for CWT ? Matlab toolbox and Python packages don't allow for such transform, and I was wondering about theoritical rational here. Thank you
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Because they have compact support implying a low localization in frequency domain. Yannick Daviaux
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I am a new leaner.
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Python first, hands down. Why? You can do more with it beyond statistics than other software, and you want to use software to make your life easier. Trust. Check out automatetheboringstuff.com and then branch out from there. Plenty of YouTube help as well. You're also best off learning R for statistics. Many similarities with Python. Don't both with SPSS as the ceiling is way too low, especially once you move into multilevel models.
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Hi everyone
i would like know , how i can add module (openpyxl: module for read or write excel file ) in python for script on Abaqus ( i use python 2.7 version for abaqus 6.14)
thanks
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Answer
1. Finding the path of Abaqus python.exe file, the last part of document path is like:
%\SIMULIA\EstProducts\2022\win_b64\tools\SMApy\python2.7.
2. Editing the environment variables and adding the path of the file to the PATH variable as the figure below.
📷📷
3. If there are multiple versions of python rename the python.exe in the location above or rename others, which will be the command used in the command line (CMD).
4. Go to the file location and use the command python27(here) setup.py install to install the setuptool.
📷
5. Go to the file location of openpyxl and use the same python27(here) setup.py install command to install.
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I would like to simulate a congestion scenario using SUMO-TraCi interface. I was able to create the network layout and a few cars. How to generate an increasing number of vehicles moving at different speeds? How to extract the average speed from SUMO to use in python to plot the results?
Relevant answer
Answer
Follow these steps:
1. Define a Route: Create a route file (e.g., `myroute.rou.xml`) that defines the routes the vehicles will follow. Specify the desired start and end edges for each route.
2. Define a Vehicle Type: Create a vehicle type file (e.g., `myvtype.add.xml`) that defines the vehicle types and their properties, such as maximum speed. You can define multiple vehicle types with different speed values to simulate vehicles moving at different speeds.
3. Generate Vehicle Trajectories: Use the `randomTrips.py` script provided with SUMO to generate vehicle trajectories. This script allows you to specify the number of vehicles to generate, their depart times, and their routes. For example, you can gradually increase the number of vehicles generated over time.
Here's an example command to generate vehicles using `randomTrips.py`:
````
randomTrips.py -n mynetwork.net.xml -r myroute.rou.xml -e 1000 -o mytrips.trips.xml --additional-files myvtype.add.xml
```
This command generates 1000 trips (`-e 1000`) based on the defined route file, and the additional vehicle type file is specified with `--additional-files`.
4. Run SUMO Simulation: Launch the SUMO simulation using the generated vehicle trajectories:
````
sumo-gui -n mynetwork.net.xml -r mytrips.trips.xml -a myvtype.add.xml
```
This command opens the SUMO-GUI with the network layout, vehicles, and simulation settings. You can visualize the simulation in real-time and observe the congestion scenario.
To extract the average speed from SUMO and use it in Python to plot the results, you can utilize the TraCI interface and follow these steps:
1. Import TraCI in Python: Import the TraCI library in your Python script to establish a connection with the SUMO simulation and retrieve simulation data.
````python
import traci
```
2. Connect to SUMO: Establish a connection with the running SUMO simulation within your Python script.
````python
traci.init(port=<port_number>)
```
3. Retrieve Vehicle Speeds: Within a simulation loop, retrieve the speeds of the vehicles at each time step using the `traci.vehicle.getSpeed()` function. Store the speeds in a list or any data structure for further analysis.
````python
speeds = []
for step in range(simulation_steps):
traci.simulationStep()
vehicle_ids = traci.vehicle.getIDList()
for vehicle_id in vehicle_ids:
speed = traci.vehicle.getSpeed(vehicle_id)
speeds.append(speed)
```
4. Calculate Average Speed: After the simulation loop, calculate the average speed from the collected speed data.
````python
average_speed = sum(speeds) / len(speeds)
```
5. Plot the Results: Use a plotting library such as Matplotlib to visualize the results. You can plot the speed values over time or create histograms to analyze the distribution of speeds.
````python
import matplotlib.pyplot as plt
# Plotting speed over time
time = range(simulation_steps)
plt.plot(time, speeds)
plt.xlabel('Time Step')
plt.ylabel('Speed')
plt.title('Vehicle Speed Over Time')
# Plotting speed distribution
plt.hist(speeds, bins=20)
plt.xlabel('Speed')
plt.ylabel('Frequency')
plt.title('Vehicle Speed Distribution')
```
Remember to close the TraCI connection and end the simulation when you are done:
```python
traci.close()
```
Hope it helps: credit AI.
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Hi folks!
Let's say that I have two lists / vectors "t_list" and "y_list" representing the relationship y(t). I also have numerically computed dy/dt and stored it into "dy_dt_list".
The problem is that "dy_dt_list" contains a lot of fluctuations, and that I know that it MONOTONOUSLY DECREASES out of a physical theory.
1) Is there is a simple way in R or Python to carry out a spline regression that reproduces the numerical values of dy/dt(t) in "dy_dt_list" as best it can UNDER THE CONSTRAINT that it keeps decreasing? I thus want to get a monotonously decreasing (dy/dt)_spline as the output.
2) Is there is a simple way in R or Python to carry out a spline regression that reproduces the numerical values of y(t) as best it can UNDER THE CONSTRAINT that (dy/dt)spline keeps decreasing? I thus want to get y_spline as the output, given that the above constraint is fulfilled.
I'd like to avoid having to reinvent the wheel!
P.S: I added an example to clarify things!
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Answer
Hi!
There is C-library "GNU Scientific Library" - chapter 29 "Numerical Differentiation". It's free software.
There is FORTRAN-C-...-Pyton-library "IMSL". Is it possible documentation will be sufficient supporting? Documentation is free.
Best regards.
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Currently, I have a global variable array and I can also plot it in the calibration window but I want to plot each data sample by a delay of 2.5 mili Seconds which means after one data sample next should be plotted after 2.5 mili Seconds.
and is it possible to do so in CANape Only without external software such as MATLAB-Simulink or Python etc...
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Answer
Follow these steps:
```python
import clr
from System import TimeSpan
# Load the CANape COM library
clr.AddReference('CANape7')
# Import CANape types
from CANape import CANape
def plot_signal_with_delay(signal_name):
# Create a CANape object
app = CANape()
try:
# Connect to CANape instance
app.Connect()
# Open the calibration window
# Create the measurement object for the specified signal
measurement = app.Measurement.CreateMeasurement(signal_name)
# Set the measurement mode to continuous
measurement.Mode = 1 # Continuous mode
# Set the measurement delay to 2.5 milliseconds
measurement.Delay = TimeSpan.FromMilliseconds(2.5)
# Start the measurement
measurement.Start()
# Wait for user interaction (e.g., press Ctrl+C) to stop the measurement
input("Press Enter to stop the measurement...")
# Stop the measurement
measurement.Stop()
finally:
# Disconnect from CANape instance
app.Disconnect()
# Example usage
signal_name = "MySignal"
plot_signal_with_delay(signal_name)
```
You should have CANape COM library (`CANape7.dll`) installed and available in the Python environment. You may need to adjust the DLL path in the `clr.AddReference()` line if it's located in a different directory.
Replace `"MySignal"` with the name of the signal you want to plot. The code opens the calibration window, creates a measurement object for the specified signal, sets the measurement mode to continuous, and sets the delay between each data sample to 2.5 milliseconds. The measurement is then started, and it will continue until you stop it by pressing Enter.
Hope it helps
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Need help with an unsupervised deep image stacking project. Image stacking is a commonly used technique in astrophotography and other areas to improve the signal-to-noise ratio of images. The process works by first aligning a large number of short exposure images and then averaging them which reduces the noise variance of individual pixels. I have to do this process with neural networks by predicting a distortion field for each image and using a consistency objective that tries to maximize the coherence between the undistorted images in the stack and the final output. I need some learning materials for performing image stacking preferably in python and make a neural network. I already have experiences with training object classification and detection models and have worked on different YOLO models.
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Due to the specific characteristics and complicated contents of remote sensing (RS) images, remote sensing image retrieval (RSIR) is always an open and tough research topic in the RS community. There are two basic blocks in RSIR, including feature learning and similarity matching. In this paper, we focus on developing an effective feature learning method for RSIR. With the help of the deep learning technique, the proposed feature learning method is designed under the bag-of-words (BOW) paradigm.
Regards,
Shafagat
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Hello everyone,
Can anyone provide me with some ideas or any code for how to find a 95% confidence level plot it over a spatial plot using Python? Provided the data is in netcdf format.
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Mohammad Imam Thanks for the solution.
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I want to cluster multiple pdb files with respect to one reference pdb. I have to use Align > all this to *Ca in Pymol. However, how could i do this via scripting in Pymol? As I have multiple sets of pdb files with their own reference pdb files. Is it possible to do the same in Python via Jupyter Notebook in Pymol?
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Example script that demonstrates how to align and cluster multiple PDB files with respect to a reference PDB file using PyMOL and Python:
```python
import pymol
# Start PyMOL
pymol.finish_launching(['pymol', '-qc'])
# Load the reference PDB file
pymol.cmd.load('reference.pdb', 'reference')
# Iterate over the list of PDB files to align and cluster
pdb_files = ['file1.pdb', 'file2.pdb', 'file3.pdb']
for pdb_file in pdb_files:
# Load the current PDB file
pymol.cmd.load(pdb_file, 'current')
# Align all atoms to the reference
pymol.cmd.align('current', 'reference')
# Cluster the aligned structure based on CA atoms
pymol.cmd.cluster('current', cutoff=3.0, selection='name CA')
# Save the aligned and clustered structure
pymol.cmd.save('aligned_clustered_' + pdb_file, 'current')
# Delete the current structure from the PyMOL session
pymol.cmd.delete('current')
# Quit PyMOL
pymol.cmd.quit()
```
In this example, you would replace `'reference.pdb'` with the path to your reference PDB file. Similarly, update `'file1.pdb'`, `'file2.pdb'`, and `'file3.pdb'` with the paths to your own PDB files.
The script iterates over each PDB file, loading it into PyMOL as the `'current'` object. It then aligns the `'current'` structure to the `'reference'` structure using the `align()` function. The alignment is performed on all atoms.
After the alignment, the script clusters the aligned structure based on CA atoms using the `cluster()` function. The `cutoff` parameter specifies the clustering distance threshold.
Hope it helps
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Hello,
I have performed MM-PBSA calculation of a protein-ligand complex. I utilised approx 750 frames (out of a total of 15000 frames) to compute the free enrgy change of binding. Then, I used a python code to compute ACF of the total delta G binding. But, the obtained ACF plot is not showing exponential decay feature exactly. I am not able to figure it out. I am attaching my plot here.
Any suggestions would be highly appreciated.
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you need a dataset that contains the free energy values at different time points. Assuming you have such a dataset, here's an example Python code that calculates the auto-correlation function using the `numpy` library:
```python
import numpy as np
def auto_correlation(data):
"""
Calculates the auto-correlation function of a given dataset.
Parameters:
data (numpy array): 1D array of free energy values.
Returns:
acf (numpy array): Auto-correlation function.
"""
n = len(data)
mean = np.mean(data)
data_normalized = data - mean
acf = np.correlate(data_normalized, data_normalized, mode='full')[-n:]
acf /= (n * np.var(data))
return acf
# Example dataset (replace with your own data)
free_energy_data = np.array([1.2, 1.5, 2.1, 2.5, 2.8, 2.9, 2.7, 2.4, 2.0, 1.8])
# Calculate auto-correlation function
acf = auto_correlation(free_energy_data)
# Print the auto-correlation values
print(acf)
```
Replace as needed. Hope it helps
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I'm trying to generate ligand topology files through CHARMM FF but i'm getting this error. I installed the respective python version but error is still same
python cgenff_charmm2gmx.py UNK unk_fix.mol2 unk.str charmm36-jul2022.ff
You are using a Python version in the 2.x series. This script requires Python 3.0 or higher.
Please visit http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs to get a script for Python 3.x
Kindly help
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"cgenff_charmm2gmx.py" requires Python 3.0 or higher, but you are using a Python version in the 2.x series. To resolve this issue, you need to make sure that you are running the script with a compatible Python version.
To resolve the problem:
1. Check Python version: Confirm the version of Python installed on your system. Open a terminal or command prompt and type `python --version` or `python3 --version` to check the installed Python version. If you see a version in the 2.x series, you will need to install Python 3.x.
2. Install Python 3.x: If you don't have Python 3.x installed, you can download and install it from the official Python website (https://www.python.org/). Make sure to choose the appropriate version for your operating system.
3. Verify Python 3 installation: After installing Python 3.x, verify that it is correctly installed by running `python3 --version` in the terminal or command prompt. This should display the installed Python 3 version.
4. Run the script with Python 3: Once Python 3.x is installed, use the `python3` command instead of `python` to run the script. For example, in your case, you would run the following command:
````
python3 cgenff_charmm2gmx.py UNK unk_fix.mol2 unk.str charmm36-jul2022.ff
```
Hope it helps
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I have to use Orbbec Femto Mega for the motion tracking applications, but I cannot find proper documentation regarding the camera interface with Python or C++. If somebody can give me an idea of where I can get the documentation or which libraries I can use, it would be great. I already tried OpenNI but it's not recognizing the camera.
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Try anyone of these.
1. Orbbec Developer Portal: Visit the Orbbec Developer Portal (https://developer.orbbec.com/) for official documentation, including API references, tutorials, and sample code. It provides resources specific to Orbbec cameras, including the Femto Mega.
2. Orbbec GitHub Repository: Explore the Orbbec GitHub repository (https://github.com/orbbec) for open-source projects and sample code related to their cameras. You may find examples and libraries that demonstrate how to interface with the Femto Mega camera using Python or C++.
3. Open3D: Open3D (http://www.open3d.org/) is an open-source library for 3D data processing, including point cloud and RGB-D data. It supports various 3D cameras, including Orbbec cameras. Open3D provides an easy-to-use Python interface, and you can refer to their documentation and examples to learn how to integrate the Femto Mega camera with your Python application.
4. PyOpenNI: PyOpenNI (https://github.com/jmendeth/PyOpenNI) is a Python wrapper for the OpenNI library, which provides support for various depth cameras, including some Orbbec models. Although you mentioned that you've already tried OpenNI, you could give PyOpenNI a try as it might have additional compatibility or fixes for the Femto Mega camera.
5. Orbbec Community Forum: Join the Orbbec Community Forum (https://3dclub.orbbec3d.com/) to connect with other developers who are working with Orbbec cameras. You can ask questions, seek guidance, and share your experiences related to the Femto Mega camera. The community members and Orbbec staff can provide insights and assistance based on their expertise.
Hope it helps
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Hello, I'm new in the Markov Switching autoregressive model. I need some help with implementing the MSIH-AR model in Python. This model requires introducing regime state variables into the intercept and error terms of the equation, as well as the heteroscedasticity in the error term. However, the statsmodels.api.tsa.MarkovAutoregression object in Python uses the mean form(i.e., the deviation form) of the equation to implement the MS-AR model (i.e., the MSM-AR model) by default. This makes me very confused. How can I use statsmodels.api.tsa.MarkovAutoregression to implement the MSIH-AR model? Thank you for your kind assistance. If possible, please also tell me how to implement MSIH-AR model using either Matlab, r, or EViews.
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Mohammad Imam Thank you for your reply. I appreciate your interest and feedback on my question. Since researchgate does not allow editing formulas, I have also asked the same question on github. You can check this link https://github.com/statsmodels/statsmodels/issues/9060 to see my detailed problem. In summary, I am trying to compare the performance of different forms of MS-AR models before running them on my data. Comparing the performance of different forms of MS-AR models before running them is a common practice in the literature. I am following the classification of MS-VAR models in Krolzig, H.-M. 1997. Markov-switching vector autoregressions: Modelling, statistical inference and an application to the business cycle analysis. The attached figure is from this book, and although it is for MS-VAR models, I think it can be applied to MS-AR models as well. It seems that statsmodels.api.tsa.MarkovAutoregression can only implement the models with switching means. However, the MSIH-AR model I try to estimate is like this with Markov-switching intercepts and variances but without Markov-switching means. Is there a way to implement the other models and compare the performance? Thank you for your help and guidance.
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Dear Expert, My question is, is there any way to call or couple the code file (Matlab or Python) in the fluent simulation? if yes please let me know the what is procedure and steps. I created an ann model based on the weight and bias function and I want to know how can i couple or add directly this file to the fluent just like the UDF function of one property or function.
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Do you have any information about this?
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I am working on a research project involving a system of differential equations with one ordinary differential equation (ODE) and two partial differential equations (PDEs).
I would like to discuss methods and approaches for solving this system efficiently using Numerical method and Machine Learning.
Can you recommend Python/Matlab code for using numerical techniques and ML
Any guidance or references would be greatly appreciated.
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That's a good question. I rarely do that so not at answering this but you can find some nice tutorials for that from experts in this field.
Tutorials:
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I have a netCDF4 (.nc) file having ocean SST data, with coordinates (lat, lon, time). I want to predict and plot maps for the future. How can I do this using python?
Please recommend a python code for time series forecasting based on this approach.
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This is not a programming question. It's a time-series question. Imagine measuring temperature in your back yard every hour for a day. You could use that to make predictions, but they might not be very useful, because weather changes from day to day. So, you need more than a day. Maybe you measure for 3 days. That would be better. But maybe those were 3 warm days, which are followed by 3 cool days. Etc.
Depending on your background, you might start by reading books on time-series analysis. Then move on to books about ocean physics. And then climate physics. You will soon see that statistical prediction is a weak approach, and that dynamical models are required. That takes you from the domain of reading and plotting with python to the domain of building PhD-level scientific and computing skills. The latter go way beyond plotting with python; you'll need to deploy supercomputers to run models that were took many person-decades to develop and take person-years to learn to run. Oh, and the end result will be a model prediction that will not agree with other model predictions to within the error bars we want for climate prediction.