framed | framed : a metabolic modeling package for python | 3D Animation library
kandi X-RAY | framed Summary
kandi X-RAY | framed Summary
framed: a metabolic modeling package for python
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- R Construct a minimal minimum constraint that minimizes the model
- Calculate molecular weight from formula
- Return a solver instance
- Get the default solver
- Finds gaps in the model
- Returns a dictionary of metabolite reactions
- A matrix of stoichiometry
- R Compute biomass reaction
- Convert the given constraints into a dictionary
- Load an SBML model
- Calculate the objective function for each organism
- Find unbalanced reactions
- Generate a GIMME for a given gene expression
- Create a list of strains along the reaction envelope
- Print exchange rates
- Compute the CFBBA
- Compute the flux of a gene expression
- Write the model to a file
- Simulate an ensemble
- Plots highlighen ensembles in KEGG pathways
- Fill a gap filling gap fill in the model
- R Calculates the net concentration for a given model
- Compute the TFA for a given model
- Solve the objective
- Plot flux envelope
- Solve the problem
framed Key Features
framed Examples and Code Snippets
Community Discussions
Trending Discussions on framed
QUESTION
What is the difference between Arrow IPC and Feather?
The official documentation says:
Version 2 (V2), the default version, which is exactly represented as the Arrow IPC file format on disk. V2 files support storing all Arrow data types as well as compression with LZ4 or ZSTD. V2 was first made available in Apache Arrow 0.17.0.
While vaex, a pandas alternative, has two different functions, one for Arrow IPC and one for Feather. polars, another pandas alternative, indicate that Arrow IPC and Feather are the same.
...ANSWER
Answered 2021-Jun-09 at 20:18TL;DR There is no difference between the Arrow IPC file format and Feather V2.
There's some confusion because of the two versions of Feather, and because of the Arrow IPC file format vs the Arrow IPC stream format.
For the two versions of Feather, see the FAQ entry:
What about the “Feather” file format?
The Feather v1 format was a simplified custom container for writing a subset of the Arrow format to disk prior to the development of the Arrow IPC file format. “Feather version 2” is now exactly the Arrow IPC file format and we have retained the “Feather” name and APIs for backwards compatibility.
So IPC == Feather(V2). Some places refer to Feather mean Feather(V1) which is different from the IPC file format. However, that doesn't seem to be the issue here: Polars and Vaex appear to use Feather to mean Feather(V2) (though Vaex slightly misleadingly says "Feather is exactly represented as the Arrow IPC file format on disk, but also support compression").
Vaex exposes both export_arrow
and export_feather
. This relates to another point of Arrow, as it defines both an IPC stream format and an IPC file format. They differ in that the file format has a magic string (for file identification) and a footer (to support random access reads) (documentation).
export_feather
always writes the IPC file format (==FeatherV2), while export_arrow
lets you choose between the IPC file format and the IPC stream format. Looking at where export_feather
was added I think the confusion might stem from the PyArrow APIs making it obvious how to enable compression with the Feather API methods (which are a user-friendly convenience) but not with the IPC file writer (which is what export_arrow
uses). But ultimately, the format being written is the same.
QUESTION
I want to modify the frame-delay in animated GIF files using the PropertyItems in System.Drawing.Image. This works well, but I'm not able to save the changes to file.
Thx in advance, Peter
Win10 x64; .NET Framework 4.6.2
...ANSWER
Answered 2021-Jun-07 at 21:35After Microsoft apparently didn't find it necessary to implement the GDI+ components in a presentable way, I have solved the problem now completely differently and low-level.
Thanks to Bjørn for this excellent solution (it's a complete low-level Gif-Editor with UI): https://www.codeproject.com/Articles/1042433/Manipulating-GIF-Color-Tables?msg=5810217#xx5810217xx
QUESTION
I'm trying to implement the paper Integrated optimization of underwater acoustic ship-radiated noise recognition based on two-dimensional feature fusion.
My biggest problem is transforming .wav
files to 2d arrays.
In the paper, it's mentioned
Each originally recorded signal in the database is framed using the hamming window of length 2048 with 50% overlap. With sampling frequency fs=52734 Hz, each sample lasts approximately 40 ms
and also
7 levels of WP decomposition with fourth-order Symlet wavelet is utilized to decompose each raw sample into 128 subbands.
I really appreciate any help in understanding and implementing this using Python.
...ANSWER
Answered 2021-May-21 at 14:06You can compute overlapping windows using librosa.utils.frame, with window_length=2048 and hop_length=1024 (50% overlap). The window function can be computed using librosa.filters.get_window with window="hamming"
Each window from the frame function you multiply by the window function. Then you can use pywt.wavedec with wavelet="sym" and level=7 to get the output for each frame. It should have 128 dimensions.
QUESTION
I am trying to create video files with ffmpeg using frames dynamically created on a separate thread.
While I can create those frames and store them on disk/memory, I'd like to avoid that passage since the amount/size of the frames can be high and many "jobs" could be created with different format or options. But, also importantly, I'd like to better understand the logic behind this, as I admit I've not a very deep knowledge on how thread/processing actually works.
Right now I'm trying to create the QProcess in the QThread object, and then run the image creation thread as soon as the process is started, but it doesn't seem to work: no file is created, and I don't even get any output from standard error (but I know I should, since I can get it if I don't use the thread).
Unfortunately, due to my little knowledge on how QProcess deals with threads and piping (and, obviously, all possible ffmpeg options), I really don't understand how can achieve this.
Besides obviously getting the output file created, the expected result is to be able to launch the encoding (and possibly queue more encodings in the meantime) while keeping the UI responding and get notifications of the current processing state.
...ANSWER
Answered 2021-May-11 at 20:50It turns out that I was partially right and wrong.
- ffmpeg has multiple levels and amounts of internal buffering, depending on input/output formats, filters and codecs: I just didn't create enough frames to see that happening;
- interaction with the QProcess should happen in the thread in which it was created;
- for that reason, data cannot be directly written to the write channel from a different thread, so signals must be used instead;
- the write channel must be closed (from its same thread) when all data has been written in order to ensure completion of the encoding;
Considering the above, I only use the thread to create the images, then emit a signal with the saved QByteArray of each image; finally, after image creation is completed I wait for the actual completion (based on the showinfo
filter output) so that the thread is actually considered finished at that point. Some optimization could be used to queue further image creation in case of multiple jobs, but considering that it probably won't improve performance that much, I prefer the current approach.
Here is the revised code, I tested with different formats and it seems to work as expected.
QUESTION
I'm pretty new working on python and this is my first "big" project. This is what I have worked on for the day. I am trying to work on this project that randomly generates a name when you click on a category and press the generate button. It randomly generates one name but when I press the generate button again it doesn't display another name. That's what I'm trying to figure out. Also if anyone doesn't mind, how can I check a box and generate a name on that category.
Thank you very much
...ANSWER
Answered 2021-May-11 at 12:44Your name choices are more naturally organized as Radiobutton
widgets.
QUESTION
In my project, I want to play a GIF in a PictureBox.
I need to play all Frames the GIF animation contains, then stop the animation.
I'm using the ImageAnimator class to animate a GIF Image, I just don't know how to stop it.
...ANSWER
Answered 2021-May-02 at 19:49To keep track of the current Frame that's being drawn on your PictureBox, you need a Field to store the current progress and compare it with the number of Frames that the animation contains.
When the progress reaches the last Frame (or any other Frame before the last, whatever is needed), you stop the animation calling ImageAnimator.StopAnimate().
To start the animation, you first check whether ImageAnimator.CanAnimate() (it may not be able to animate the Image you specified). If it can, then you call ImageAnimator.Animate(), passing to the method the Image object and the address of the method that handles the FrameChanged
event.
This handler is used to check whether the animation should continue. If all conditions are met (not all Frames have been drawn), Invalidate() the Control used to show the animation and, in its Paint
event handler, call ImageAnimator.UpdateFrames() to change the current Frame, then e.Graphics.DrawImage() to draw the Image (drawing the Frame that is now the current).
► As you can see in the visual example, I'm using a Button (btnAnimate
) to start the animation. You can move that code to the Form.Shown
event handler, if you prefer.
► I've added a loop counter, in case the animation should loop more than once.
This is how it visually works:
QUESTION
I am sorry for how I have framed the question in the title but I have started programming very recently so once again, I am really sorry.
I am developing a project with React js as my front-end and node js as my backend, I have been successful in doing some basic test api calls to confirm the connection between the two but now, how am I supposed to actually process different actions. For example, while a user is logging in, I need to first check if they are an existing user or not, sign them in if they are not, deleting a user account, changing username, etc.
I tried very hard to look for relevant articles but all I can find are basic "one-time" api calls, what am I supposed to do for an entire batch of operations? From what I have understood, the process of sending a request from React to getting it processed in Node js is like this:
...ANSWER
Answered 2021-Apr-30 at 06:23This question is really broad, so I'm going to focus in on this part at a high level:
I tried very hard to look for relevant articles but all I can find are basic "one-time" api calls, what am I supposed to do for an entire batch of operations?
I'm guessing when you talk about requests and APIs you're talking about HTTP requests and REST APIs, which are fundamentally "stateless" kinds of things; HTTP requests are self-contained, and the backend doesn't have to keep track of any application state between requests in order to speak HTTP.
But backend applications usually do maintain state, often in the form of databases. For example, many REST APIs expose CRUD (create, read, update, and delete) operations for important business entities — in fact, Stack Overflow probably does exactly this for answers. When I post this answer, my browser will probably send some kind of a "create" request, and when I inevitably notice and fix a typo I will send some kind of "update" request. When you load it in your browser, you will send a "read" request which will get the text of the answer from Stack Overflow's database. Stack Overflow's backend keeps track of my answer between the requests, which makes it possible to send it to many users as part of many different requests.
Your frontend will have to do something similar if your project does things which involve multiple interdependent requests — for example, you would need to keep track of whether the user is authenticated or not in order to show them the login screen, and you would need to hold onto their authentication token to send along with subsequent requests.
Edit: Let's walk through a specific example. As a user, I want to be able to create and read notes. Each note should have a unique ID and a string for its text. On the backend, we'll have a set of CRUD endpoints:
QUESTION
I have created a side class to help me manage functions that i reuses in all of my GUI JFrames
i am using an undecorated JFrame, and i have added a simple functions to be able to drag it around
...ANSWER
Answered 2021-Apr-20 at 13:36this
refers to the most inner class you currently are, so the anonymous MouseAdapter
.
Use EntranceScreen.this
instead.
QUESTION
I'm trying to do a more complex (for me) filter with 2 different categories (hopefully more), frameBrand & frameColor. I want to filter down to a specific brand, then use those results to filter colors until I have a more specific/narrow search. I'm struggling with filtering 2 categories
With my example JSON below, I'd like to click a brand checkbox to get "anne klein" frames then click a color checkbox "brown" to view the "anne klein - brown" frame. 2 checkboxes each from different "categories". Ideally, I'd be able to expand this to use other categories, like checkboxes for price. I've used StackOverflow to get where I'm at with .filter but haven't seen much with multiple categories and checkboxes using Angular.
...ANSWER
Answered 2021-Apr-20 at 10:54I'd simplify you logic.
Instead of doing this with FormGroup
of FormArrays
(unless that is not requirement) the best here would be to create FilterComponent
which accepts as input exemplary object
type CheckboxFilter = { name: string, isChecked: boolean }
. Probably you could add id
if neccessary.
Having that created add Output
to your FilterComponent
.
Now you add to handlers for that BrandChanged
and ColorChanged
. Based on that you are able to store selected filters and apply them on your frames.
That even allows you to make it more reacive way.
You could decalre BehaviourSubject
for both Brand
and Color
and once there is event you could manipulate subject.
Later just combainLatest
of your frames that came from JSON file or API and apply do it like this:
QUESTION
In my Nativescript Vue application changed from tns-core-modules
to @nativescript/core
and now I'm facing some issues. I created a Modal Service similar to this video. There I used the import :
ANSWER
Answered 2021-Apr-16 at 02:47The imports is slightly different on Nativescript 8
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Install framed
You can use framed like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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