dmipy | open source toolbox for reproducible diffusion MRI | Machine Learning library

 by   AthenaEPI Python Version: 1.0.5 License: MIT

kandi X-RAY | dmipy Summary

kandi X-RAY | dmipy Summary

dmipy is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Machine Learning, Deep Learning applications. dmipy has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. However dmipy has 4 bugs. You can install using 'pip install dmipy' or download it from GitHub, PyPI.

The Dmipy software package facilitates the reproducible estimation of diffusion MRI-based microstructure features. It does this by taking a completely modular approach to Microstructure Imaging. Using Dmipy you can design, fit, and recover the parameters of any multi-compartment microstructure model in usually less than 10 lines of code. Created models can be used to simulate and fit data for any PGSE-based dMRI acquisition, including single shell, multi-shell, multi-diffusion time and multi-TE acquisition schemes. Dmipy's main features include:. Human Connectome Project Data Interface Dmipy enables you to directly download any HCP subject data using your own credentials. Numba-Accelerated, Multi-Core processing Dmipy takes heavy advantage of Python's pathos multi-core processing and numba function compilation. Documentation on Tissue and Microstructure Models We include documentation and illustrations of all tissue models and parameter distributions, as well as example implementations and results on HCP data for Ball and Stick, Ball and Racket, NODDI-Watson/Bingham, AxCaliber, Spherical Mean models and more. Dipy Compatibility Dmipy is designed to be complementary for Dipy users. Dipy gradient tables can be directly used in Dmipy models, Dipy models can be used to give initial parameter guesses for Dmipy optimization, and Dmipy models that estimate Fiber Orientation Distributions (FODs) can be visualized and used for tractography in Dipy. Dmipy allows the user to do Microstructure Imaging research at the highest level, while the package automatically takes care of all the coding architecture that is needed to fit a designed model to a data set. The Dmipy documentation can be found at If you use Dmipy for your research publications, we kindly request you cite this package at the reference at the bottom of this page.
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            kandi-support Support

              dmipy has a low active ecosystem.
              It has 50 star(s) with 17 fork(s). There are 20 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 40 open issues and 24 have been closed. On average issues are closed in 68 days. There are 9 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of dmipy is 1.0.5

            kandi-Quality Quality

              OutlinedDot
              dmipy has 4 bugs (2 blocker, 0 critical, 1 major, 1 minor) and 495 code smells.

            kandi-Security Security

              dmipy has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              dmipy code analysis shows 0 unresolved vulnerabilities.
              There are 3 security hotspots that need review.

            kandi-License License

              dmipy is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              dmipy releases are available to install and integrate.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions are available. Examples and code snippets are not available.
              dmipy saves you 4389 person hours of effort in developing the same functionality from scratch.
              It has 9295 lines of code, 527 functions and 78 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed dmipy and discovered the below as its top functions. This is intended to give you an instant insight into dmipy implemented functionality, and help decide if they suit your requirements.
            • Fit the model using the given acquisition scheme
            • Checks that the acquisition scheme contains b0s
            • Check if Tortuosity constraint is set
            • Checks if all volume fractions are fixed
            • Perform a single shell fitting of a single shell
            • Set a fixed parameter
            • Adds a fixed parameter array
            • Add a fixed parameter value to the model
            • Precompute signal grid
            • Run IVIM Dstar - fixed algorithm
            • Visualise the acquisition
            • Visualize correlation coefficient
            • Calculate a DmipyAcquisitionScheme
            • Stochastic objective function
            • Estimate a DmipyAcquisitionScheme
            • Calculate the spherical mean of the sphere
            • Simulate a signal
            • Construct the convolution kernel for the Fourier transform
            • Add a fractional parameter to the model
            • Link to GitHub role
            • Return the FOD of the FOD of the FOD
            • Constructs the convolution kernel matrix for the objective function
            • Visualize the model setup
            • Compute objective function
            • Write API documentation to outdir
            • Parse the docstring section
            • Returns the spherical harmonic symmetry representation of the spherical harmonic
            Get all kandi verified functions for this library.

            dmipy Key Features

            No Key Features are available at this moment for dmipy.

            dmipy Examples and Code Snippets

            No Code Snippets are available at this moment for dmipy.

            Community Discussions

            QUESTION

            Using RNN Trained Model without pytorch installed
            Asked 2022-Feb-28 at 20:17

            I have trained an RNN model with pytorch. I need to use the model for prediction in an environment where I'm unable to install pytorch because of some strange dependency issue with glibc. However, I can install numpy and scipy and other libraries. So, I want to use the trained model, with the network definition, without pytorch.

            I have the weights of the model as I save the model with its state dict and weights in the standard way, but I can also save it using just json/pickle files or similar.

            I also have the network definition, which depends on pytorch in a number of ways. This is my RNN network definition.

            ...

            ANSWER

            Answered 2022-Feb-17 at 10:47

            You should try to export the model using torch.onnx. The page gives you an example that you can start with.

            An alternative is to use TorchScript, but that requires torch libraries.

            Both of these can be run without python. You can load torchscript in a C++ application https://pytorch.org/tutorials/advanced/cpp_export.html

            ONNX is much more portable and you can use in languages such as C#, Java, or Javascript https://onnxruntime.ai/ (even on the browser)

            A running example

            Just modifying a little your example to go over the errors I found

            Notice that via tracing any if/elif/else, for, while will be unrolled

            Source https://stackoverflow.com/questions/71146140

            QUESTION

            Flux.jl : Customizing optimizer
            Asked 2022-Jan-25 at 07:58

            I'm trying to implement a gradient-free optimizer function to train convolutional neural networks with Julia using Flux.jl. The reference paper is this: https://arxiv.org/abs/2005.05955. This paper proposes RSO, a gradient-free optimization algorithm updates single weight at a time on a sampling bases. The pseudocode of this algorithm is depicted in the picture below.

            optimizer_pseudocode

            I'm using MNIST dataset.

            ...

            ANSWER

            Answered 2022-Jan-14 at 23:47

            Based on the paper you shared, it looks like you need to change the weight arrays per each output neuron per each layer. Unfortunately, this means that the implementation of your optimization routine is going to depend on the layer type, since an "output neuron" for a convolution layer is quite different than a fully-connected layer. In other words, just looping over Flux.params(model) is not going to be sufficient, since this is just a set of all the weight arrays in the model and each weight array is treated differently depending on which layer it comes from.

            Fortunately, Julia's multiple dispatch does make this easier to write if you use separate functions instead of a giant loop. I'll summarize the algorithm using the pseudo-code below:

            Source https://stackoverflow.com/questions/70641453

            QUESTION

            How can I check a confusion_matrix after fine-tuning with custom datasets?
            Asked 2021-Nov-24 at 13:26

            This question is the same with How can I check a confusion_matrix after fine-tuning with custom datasets?, on Data Science Stack Exchange.

            Background

            I would like to check a confusion_matrix, including precision, recall, and f1-score like below after fine-tuning with custom datasets.

            Fine tuning process and the task are Sequence Classification with IMDb Reviews on the Fine-tuning with custom datasets tutorial on Hugging face.

            After finishing the fine-tune with Trainer, how can I check a confusion_matrix in this case?

            An image of confusion_matrix, including precision, recall, and f1-score original site: just for example output image

            ...

            ANSWER

            Answered 2021-Nov-24 at 13:26

            What you could do in this situation is to iterate on the validation set(or on the test set for that matter) and manually create a list of y_true and y_pred.

            Source https://stackoverflow.com/questions/68691450

            QUESTION

            CUDA OOM - But the numbers don't add upp?
            Asked 2021-Nov-23 at 06:13

            I am trying to train a model using PyTorch. When beginning model training I get the following error message:

            RuntimeError: CUDA out of memory. Tried to allocate 5.37 GiB (GPU 0; 7.79 GiB total capacity; 742.54 MiB already allocated; 5.13 GiB free; 792.00 MiB reserved in total by PyTorch)

            I am wondering why this error is occurring. From the way I see it, I have 7.79 GiB total capacity. The numbers it is stating (742 MiB + 5.13 GiB + 792 MiB) do not add up to be greater than 7.79 GiB. When I check nvidia-smi I see these processes running

            ...

            ANSWER

            Answered 2021-Nov-23 at 06:13

            This is more of a comment, but worth pointing out.

            The reason in general is indeed what talonmies commented, but you are summing up the numbers incorrectly. Let's see what happens when tensors are moved to GPU (I tried this on my PC with RTX2060 with 5.8G usable GPU memory in total):

            Let's run the following python commands interactively:

            Source https://stackoverflow.com/questions/70074789

            QUESTION

            How to compare baseline and GridSearchCV results fair?
            Asked 2021-Nov-04 at 21:17

            I am a bit confusing with comparing best GridSearchCV model and baseline.
            For example, we have classification problem.
            As a baseline, we'll fit a model with default settings (let it be logistic regression):

            ...

            ANSWER

            Answered 2021-Nov-04 at 21:17

            No, they aren't comparable.

            Your baseline model used X_train to fit the model. Then you're using the fitted model to score the X_train sample. This is like cheating because the model is going to already perform the best since you're evaluating it based on data that it has already seen.

            The grid searched model is at a disadvantage because:

            1. It's working with less data since you have split the X_train sample.
            2. Compound that with the fact that it's getting trained with even less data due to the 5 folds (it's training with only 4/5 of X_val per fold).

            So your score for the grid search is going to be worse than your baseline.

            Now you might ask, "so what's the point of best_model.best_score_? Well, that score is used to compare all the models used when searching for the optimal hyperparameters in your search space, but in no way should be used to compare against a model that was trained outside of the grid search context.

            So how should one go about conducting a fair comparison?

            1. Split your training data for both models.

            Source https://stackoverflow.com/questions/69844028

            QUESTION

            Getting Error 524 while running jupyter lab in google cloud platform
            Asked 2021-Oct-15 at 02:14

            I am not able to access jupyter lab created on google cloud

            I created one notebook using Google AI platform. I was able to start it and work but suddenly it stopped and I am not able to start it now. I tried building and restarting the jupyterlab, but of no use. I have checked my disk usages as well, which is only 12%.

            I tried the diagnostic tool, which gave the following result:

            but didn't fix it.

            Thanks in advance.

            ...

            ANSWER

            Answered 2021-Aug-20 at 14:00

            QUESTION

            TypeError: brain.NeuralNetwork is not a constructor
            Asked 2021-Sep-29 at 22:47

            I am new to Machine Learning.

            Having followed the steps in this simple Maching Learning using the Brain.js library, it beats my understanding why I keep getting the error message below:

            I have double-checked my code multiple times. This is particularly frustrating as this is the very first exercise!

            Kindly point out what I am missing here!

            Find below my code:

            ...

            ANSWER

            Answered 2021-Sep-29 at 22:47

            Turns out its just documented incorrectly.

            In reality the export from brain.js is this:

            Source https://stackoverflow.com/questions/69348213

            QUESTION

            Ordinal Encoding or One-Hot-Encoding
            Asked 2021-Sep-04 at 06:43

            IF we are not sure about the nature of categorical features like whether they are nominal or ordinal, which encoding should we use? Ordinal-Encoding or One-Hot-Encoding? Is there a clearly defined rule on this topic?

            I see a lot of people using Ordinal-Encoding on Categorical Data that doesn't have a Direction. Suppose a frequency table:

            ...

            ANSWER

            Answered 2021-Sep-04 at 06:43

            You're right. Just one thing to consider for choosing OrdinalEncoder or OneHotEncoder is that does the order of data matter?

            Most ML algorithms will assume that two nearby values are more similar than two distant values. This may be fine in some cases e.g., for ordered categories such as:

            • quality = ["bad", "average", "good", "excellent"] or
            • shirt_size = ["large", "medium", "small"]

            but it is obviously not the case for the:

            • color = ["white","orange","black","green"]

            column (except for the cases you need to consider a spectrum, say from white to black. Note that in this case, white category should be encoded as 0 and black should be encoded as the highest number in your categories), or if you have some cases for example, say, categories 0 and 4 may be more similar than categories 0 and 1. To fix this issue, a common solution is to create one binary attribute per category (One-Hot encoding)

            Source https://stackoverflow.com/questions/69052776

            QUESTION

            How to increase dimension-vector size of BERT sentence-transformers embedding
            Asked 2021-Aug-15 at 13:35

            I am using sentence-transformers for semantic search but sometimes it does not understand the contextual meaning and returns wrong result eg. BERT problem with context/semantic search in italian language

            by default the vector side of embedding of the sentence is 78 columns, so how do I increase that dimension so that it can understand the contextual meaning in deep.

            code:

            ...

            ANSWER

            Answered 2021-Aug-10 at 07:39

            Increasing the dimension of a trained model is not possible (without many difficulties and re-training the model). The model you are using was pre-trained with dimension 768, i.e., all weight matrices of the model have a corresponding number of trained parameters. Increasing the dimensionality would mean adding parameters which however need to be learned.

            Also, the dimension of the model does not reflect the amount of semantic or context information in the sentence representation. The choice of the model dimension reflects more a trade-off between model capacity, the amount of training data, and reasonable inference speed.

            If the model that you are using does not provide representation that is semantically rich enough, you might want to search for better models, such as RoBERTa or T5.

            Source https://stackoverflow.com/questions/68686272

            QUESTION

            How to identify what features affect predictions result?
            Asked 2021-Aug-11 at 15:55

            I have a table with features that were used to build some model to predict whether user will buy a new insurance or not. In the same table I have probability of belonging to the class 1 (will buy) and class 0 (will not buy) predicted by this model. I don't know what kind of algorithm was used to build this model. I only have its predicted probabilities.

            Question: how to identify what features affect these prediction results? Do I need to build correlation matrix or conduct any tests?

            Table example:

            ...

            ANSWER

            Answered 2021-Aug-11 at 15:55

            You could build a model like this.

            x = features you have. y = true_lable

            from that you can extract features importance. also, if you want to go the extra mile,you can do Bootstrapping, so that the features importance would be more stable (statistical).

            Source https://stackoverflow.com/questions/68744565

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install dmipy

            You can install dmipy using pypi by typing in your terminal. or you can manually. See solutions to common issues.
            python3 -m pip install dmipy
            clone repository
            python setup.py install
            To get a feeling for how to use Dmipy, we provide a few tutorial notebooks:.
            Setting up an acquisition scheme
            Simulating and fitting data using a simple Stick model
            Combining biophysical models into a Microstructure model
            Creating a dispersed and/or distributed axon bundle representation
            Imposing parameter links and constraints
            Parameter Cascading: Using a simple model to initialize a complex one
            Generalized Multi-Tissue Modeling

            Support

            Dmipy's design is completely modular and can easily be extended with new models, distributions or optimizers. To contribute, view our contribution guidelines.
            Find more information at:

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