dexp | Dataset EXploration & Processing | Data Manipulation library
kandi X-RAY | dexp Summary
kandi X-RAY | dexp Summary
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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Top functions reviewed by kandi - BETA
- 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
dexp Key Features
dexp Examples and Code Snippets
Community Discussions
Trending Discussions on dexp
QUESTION
ANSWER
Answered 2022-Mar-08 at 02:30As you pointed out, you do want geom_ribbon
:
QUESTION
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 16:24Add an await client.process_commands(message)
at the end of your on_message
event
QUESTION
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 23:43There 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
:
QUESTION
Suppose I have the following c source code, in dexp_test.c
:
ANSWER
Answered 2020-Sep-19 at 18:25You 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
QUESTION
ANSWER
Answered 2020-Aug-11 at 08:21The 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 functionlambda
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
.
QUESTION
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 04:42The 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
QUESTION
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 03:08You seem to have several issues in your code:
shannon_portf
does not existinput$rate
does not exist; butinput$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.
QUESTION
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 12:08eqn2
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.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
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Install dexp
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.
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