dexp | Dataset EXploration & Processing | Data Manipulation library

 by   royerlab Python Version: 2023.4.10.686 License: BSD-3-Clause

kandi X-RAY | dexp Summary

kandi X-RAY | dexp Summary

dexp is a Python library typically used in Utilities, Data Manipulation, Numpy applications. dexp has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install dexp' or download it from GitHub, PyPI.

dexp is a napari, CuPy, Zarr, and DASK based library for managing, processing and visualizing light-sheet microscopy datasets. It consists in light-sheet specialised image processing functions (equalisation, denoising, dehazing, registration, fusion, stabilization, deskewing, deconvolution), visualization functions (napari-based viewing, 2D/3D rendering, video compositing and resizing, mp4 generation), as well as dataset management functions (copy, crop, concatenation, tiff conversion). Almost all functions are GPU accelerated via CuPy but also have a numpy-based fallback option for testing on small datasets. In addition to a functional API, DEXP offers a command line interface that makes it very easy for non-coders to pipeline large processing jobs all the way from a large multi-terabyte raw dataset to fully processed and rendered video in MP4 format.
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            kandi-support Support

              dexp has a low active ecosystem.
              It has 20 star(s) with 4 fork(s). There are 7 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 9 open issues and 12 have been closed. On average issues are closed in 190 days. There are 3 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of dexp is 2023.4.10.686

            kandi-Quality Quality

              dexp has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              dexp is licensed under the BSD-3-Clause License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              dexp releases are not available. You will need to build from source code and install.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.
              It has 19848 lines of code, 1087 functions and 371 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed dexp and discovered the below as its top functions. This is intended to give you an instant insight into dexp implemented functionality, and help decide if they suit your requirements.
            • Volumetric rendering
            • Given a list of glob_paths
            • Creates a joined dataset from a list of paths
            • Create a dataset from a path
            • Overlay an image
            • Return the best fitting backend
            • Add overlays
            • Add a new channel
            • Generate a numpy array for a given shape
            • Removes beads from an image
            • Example example
            • Deconvents a dataset
            • Render a dataset rendering
            • Option for click
            • Denoise a butterworth image
            • Register the fusion model
            • String representation of the dataset
            • Set the number of threads
            • Deskew a dataset
            • Resize an image
            • Render the image
            • Fuse the input_dataset
            • Generic area filtering
            • Convert an image into a classic DSArray
            • Stabilizes a dataset
            • Blend an image
            Get all kandi verified functions for this library.

            dexp Key Features

            No Key Features are available at this moment for dexp.

            dexp Examples and Code Snippets

            No Code Snippets are available at this moment for dexp.

            Community Discussions

            QUESTION

            Colour area between 2 lines in ggplot in R?
            Asked 2022-Mar-08 at 02:30

            Similar questions have been asked here and here, but I can't seem to get them to work for my example. If I have a plot that looks something like this:

            ...

            ANSWER

            Answered 2022-Mar-08 at 02:30

            As you pointed out, you do want geom_ribbon:

            Source https://stackoverflow.com/questions/71389336

            QUESTION

            Discord.py - Bot does not respond to commands
            Asked 2021-Aug-01 at 16:24

            When I write the command "! LVL" The bot just doesn't react in any way. The teams used to work. I changed something and now he does not react to them. In addition, before, if I wrote a command incorrectly, then in the console the bot gave an error that such a command does not exist. Now he does not respond to more than one command, even to the built-in one !help

            But all events work correctly.

            ...

            ANSWER

            Answered 2021-Aug-01 at 16:24

            QUESTION

            Using mle2 function
            Asked 2021-Jan-31 at 07:14

            I would like to find the MLE for parameters epsilon and mu in such a model:

            $$X \sim \frac{1}{mu1}e^{-x/mu1}+\frac{1}{mu2}e^[-x/mu2}$$

            ...

            ANSWER

            Answered 2021-Jan-27 at 23:43

            There are a bunch of issues here. The primary one is that your likelihood expression is wrong (you can't log the components separately and then add them, you have to add the components and then take the log). Your bounds are also funny: the mixture probability should be [0,1] and the means should be [0, Inf].

            The other problem you have is that with the current simulation design (n=20, prob=0.01), you have a high probability of getting no points in the first mixture component (the probability of a point being in the second component is 1-0.01=0.99, so the probability that all of the points are in the second component is 0.99^20 = 82%). In this case the MLE will be degenerate (i.e., you're trying to fit a two-component mixture to a data set that essentially only has one component); in this case any of these solutions will give equivalent likelihoods:

            • prob=0, mu2=mean of the data, mu1=anything
            • prob=1, mu1=mean of the data, mu2=anything
            • mu1=mu2=mean of the data, prob=anything

            With all these solutions, where you end up will depend very sensitively on starting conditions and optimization algorithm.

            For this problem I would encourage you to use the built-in dmixexp2 function from the Renext package (which correctly implements the log-likelihood as log(p*Prob(X|exp1) + (1-p)*Prob(X|exp2))) and the formula interface to mle2:

            Source https://stackoverflow.com/questions/65874044

            QUESTION

            using R's c code in my standalone executables: "Undefined symbols"
            Asked 2020-Sep-19 at 20:24

            Suppose I have the following c source code, in dexp_test.c:

            ...

            ANSWER

            Answered 2020-Sep-19 at 18:25

            You should mention the operating system you are using.

            You need to include the appropriate headers. And tell the linker where and which libraries you want to use.

            So your source should be

            Source https://stackoverflow.com/questions/63971608

            QUESTION

            R: Maximum Likelihood Estimation of a exponential mixture using optim
            Asked 2020-Aug-11 at 08:21

            I'm trying to get the parameters w, lambda_1, lambda_2 and p from a mixture bi-exponential model, using a loglikelihood function and the optim function in R. The model is the following

            Here is the code

            ...

            ANSWER

            Answered 2020-Aug-11 at 08:21

            The original code is prone to warnings and errors since the parameters may go to invalid values easily. For example, we need w in [0, 1] and lambda > 0. Also, if a is larger than a data point, then the density becomes zero, hence infinite log likelihood.

            The code below uses some tricks to handle these cases.

            • w is converted to the range [0, 1] by the logistic function
            • lambda are converted to positive values by the exponential function.
            • Added tiny value to the likelihood to deal with cases of zero likelihood.

            Also, the data generation process has been changed so that samples are generated from one of the exponential distributions with the given probability w.

            Finally, increased the sample size since the result was not stable with n=500.

            Source https://stackoverflow.com/questions/63352807

            QUESTION

            R: Error in optim: 'list' object cannot be coerced to type 'double'
            Asked 2020-Aug-11 at 04:42

            I'm trying to get the parameters of a bi-exponential model by minimizing the Kullback-Leibler divergence using optim. The function I'm using have 3 parameters, but when I pass them to optim using par = par it throws the error "list object cannot be coerced to type 'double'", but I'm not even using lists.

            Here is the code I'm using:

            ...

            ANSWER

            Answered 2020-Aug-11 at 04:42

            The function you pass to optim needs to return a scalar value, and your kld_optim function returns the result of a call to integrate() which according to the ?integrate help page, returns a list, not a numeric value. The "value" in contained in that list under the name "value". So change your integrate() call to

            Source https://stackoverflow.com/questions/63351562

            QUESTION

            Troubleshooting an error I do not know in R/RMd/Shiny
            Asked 2020-Apr-23 at 03:08

            I am writing an interactive HTML document using RMarkdown and ShinyApp. The part I'm having problems with is supposed to take parameters for three different probability distributions (user input) and output a plotly plot which varies depending on the graphs. This plot has 3 lines, one for each probability distribution. The error I get is length(lower) == 1 is not TRUE.

            The server/ui code is as follows:

            ...

            ANSWER

            Answered 2020-Apr-23 at 03:08

            You seem to have several issues in your code:

            • shannon_portf does not exist
            • input$rate does not exist; but input$lambda does
            • the pivot_longer statement returns an error - perhaps you wanted to sort by p?
            • the functions in the sourced file should return the value (return(mk)), instead of printing it to console (print(mk))

            Below is a version that gives a plot; you may still want to tweak it a little bit... some sliders don't seem to do anything, and you could isolate calculations that don't need to be redone.

            Source https://stackoverflow.com/questions/61375880

            QUESTION

            Role of eqn3 in Fipy examples.cahnHilliard.mesh2DCoupled
            Asked 2020-Jan-08 at 12:08

            I am currently working through the examples in the fipy documentation and am trying to adapt the examples.cahnHilliard.mesh2DCoupled to perform some simulations. The link is : https://www.ctcms.nist.gov/fipy/examples/cahnHilliard/generated/examples.cahnHilliard.mesh2DCoupled.html

            It seems that the example code declares an eq3 and a dfdphi_ and does not use these equations anywhere else, even in the solution.

            From the documentation:

            ...

            ANSWER

            Answered 2020-Jan-08 at 12:08

            eqn2 and eqn3 encode, in the limit of infinitesimal time and space steps, the same equation. However, in their discretization they single out different terms for a more active role in the construction of the time step propagator.

            In the short term this should only lead to insignificant differences in the result, in the long term there may be more pronounced differences in stability and accuracy.

            That the "more natural" equation eq3 is present at all seems to be an indirect invitation to experiment with it, and perhaps to explore if the transformation in eq2 with its possible advantages is a coincidence or result of some more deeply founded idea.

            Source https://stackoverflow.com/questions/59641437

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

            Vulnerabilities

            No vulnerabilities reported

            Install dexp

            The following commands delete any existing dexp environment, recreate it, and install dexp with support for CUDA 11.2:.
            Adjust your driver version (here 11.2) to your card(s) and drivers.
            Windows users should call conda install -c conda-forge pyopencl before running the last step.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
            Find more information at:

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            Install
          • PyPI

            pip install dexp

          • CLONE
          • HTTPS

            https://github.com/royerlab/dexp.git

          • CLI

            gh repo clone royerlab/dexp

          • sshUrl

            git@github.com:royerlab/dexp.git

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