brat | Brat is a little language for people who do n't like to be

by presidentbeef C Version: Current License: No License

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | brat Summary

brat is a C library typically used in Programming Style applications. brat has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Brat is a simple little toy language that lets you do what you want. It is primarily object-oriented with first-class functions and very little syntax.

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Quality

Security

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Support

brat has a low active ecosystem.

It has 83 star(s) with 6 fork(s). There are 6 watchers for this library.

It had no major release in the last 6 months.

There are 0 open issues and 13 have been closed. On average issues are closed in 28 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of brat is current.

Quality

brat has no bugs reported.

Security

brat has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

brat does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

brat releases are not available. You will need to build from source code and install.

Installation instructions, examples and code snippets are available.

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brat Key Features

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brat Examples and Code Snippets

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Community Discussions

Trending Discussions on brat

Transfer Learning Segmentation Model Perfoming Significantly Worse on Test Data

Image data in mha brain tumor file

How move the two rows to top of data frame in a list in R?

How to resolve pandas length error for rows/columns

what happens if two objects acess the same instance variable?

Keras model's validation loss doesn't match the loss function output

I need to deserialize a complex JSON with multiple classes in POJO

U-net: TypeError: __call__() missing 1 required positional argument: 'inputs'

Importing XML to MS Access: Non standard xml?

Angular 7 Unable to include a custom typescript definition file

QUESTION

Transfer Learning Segmentation Model Perfoming Significantly Worse on Test Data

Asked 2021-Mar-18 at 21:48

I am quite new to the field of semantic segmentation and have recently tried to run the code provided on this paper: Transfer Learning for Brain Tumor Segmentation that was made available on GitHub. It is a semantic segmentation task that uses the BraTS2020 dataset, comprising of 4 modalities, T1, T1ce, T2 and FLAIR. The author utilised a transfer learning approach using Resnet34 weights.

Due to hardware constraints, I had to half the batch size from 24 to 12. However, after training the model, I noticed a significant drop in performance, with the Dice Score (higher is better) of the 3 classes being only around 5-19-11 as opposed to the reported result of 78-87-82 in the paper. The training and validation accuracies however, seem to be performing normally, just that the model does not perform well on test data, I selected the model that was produced before overfitting (validation loss starts increasing but training loss still decreasing) but yielded equally bad results.

So far I have tried:

Decreasing the learning rate from 1e-3 to 1e-4, yielded similar results
Increased the number of batches fed to the model per training epoch to 200 batches per epoch, to match the number of iterations ran in the paper since I effectively halved the batch size - (100 batches per epoch, batch size of 24)

I noticed that image augmentations were applied to the training and validation dataset to increase the robustness of the model training. Do these augmentations need to be performed on the test set in order to make predictions? There are no resizing transforms, transforms that are present are Gaussian Blur and Noise, change in brightness intensity, rotations, elastic deformation, and mirroring, all implemented using the example here.

I'd greatly appreciate help on these questions:

By doubling the number of batches per epoch, it effectively matches the number of iterations performed as in the original paper since the batch size is halved. Is this the correct approach?
Does the test set data need to be augmented similarly to the training data in order to perform predictions? (Note: no resizing transformations were performed)

...

ANSWER

Answered 2021-Mar-18 at 21:48

Technically, for a smaller batch the number of iterations should be higher for convergence. So, your approach is going to help, but it probably won't give the same performance boost as doubling the batch size.

Usually, we don't use augmentation on test data. But if the transformation applied on training and validation is not applied to the test data, the test performance will be poor, no doubt. You can try test time augmentation though, even though it's not very common for segmentation tasks https://github.com/qubvel/ttach

Source https://stackoverflow.com/questions/66697928

QUESTION

Image data in mha brain tumor file

Asked 2021-Feb-15 at 21:54

I have an MHA file and when I write

...

ANSWER

Answered 2021-Feb-15 at 21:09

According to the documentation, load(image) "Loads the image and returns a ndarray with the image’s pixel content as well as a header object."

Further down in medpy.io.load it says that image_data is "The image data as numpy array with order x,y,z,c.".

Edit: Because I was kind of curious to see what is actually in this file, I put together a quick script (heavily based on the slider demo) to take a look. I'll leave it here just in case it may be useful to someone. (Click on the "Layer" slider to select the z-coordinate to be drawn.)

Source https://stackoverflow.com/questions/66214255

QUESTION

How move the two rows to top of data frame in a list in R?

Asked 2020-Dec-17 at 04:07

There is a list of data frames that each data frame has different rows and columns. The bottom of each data frame is the total and percentage rows. I want to move the percentage row to the top (first) and the total second row in each data frame of the list. this is a data frame sample:

...

ANSWER

Answered 2020-Dec-17 at 04:07

Here are two approaches:

Source https://stackoverflow.com/questions/65334462

QUESTION

How to resolve pandas length error for rows/columns

Asked 2020-Oct-06 at 07:19

I have raised the SO Question here and blessed to have an answer from @Scott Boston.

However i am raising another question about an error ValueError: Columns must be same length as key as i am reading a text file and all the rows/columns are not of same length, i tried googling but did not get an answer as i don't want them to be skipped.

Error ...

ANSWER

Answered 2020-Oct-06 at 01:06

I couldn't figure out a pandas way to extend the columns, but converting the rows to a dictionary made things easier.

Source https://stackoverflow.com/questions/64213828

QUESTION

what happens if two objects acess the same instance variable?

Asked 2020-Jul-25 at 16:44

i have created an user defined object which accesses an instance variable and a method.Then i created an array of of 3 elements in which one reference variable has a reference to object that i initially created.now what happens to instance variable of class if both references refer to same object.why its null says ruff??

...

ANSWER

Answered 2020-Jul-25 at 06:45

Because you are calling dog1.bark() before setting dog1.name, so name is null when calling dog1.bark(). That's why dog1.bark() prints null for name

Source https://stackoverflow.com/questions/63085179

QUESTION

Keras model's validation loss doesn't match the loss function output

Asked 2020-Jun-29 at 10:49

I am working on a biomedical image segmentation project. I am using U-net model for the job. The problem is, when i train the model, the validation loss doesn't seem to be practical.

I used the dice_coef_loss as loss function, as well as, in the metric. The result of the training is the below graph. The graph clearly shows that validation loss is not following my loss function, cause the two graphs are distinguishable. Though, the train loss does follow the train dice_coef_loss values.

(The first image from the left is training and validation loss, third one is tarining and validation dice_coef_loss as metric)

The history graph of training

(Sorry i am not yet eligible to embed an image, please check the link)

Here is my model ...

ANSWER

Answered 2020-Jun-29 at 10:49

As, ZabirAlNazi suggested it was a problem of the used library. Changing the imports from keras to tensorflow.keras solved that issue.

Source https://stackoverflow.com/questions/62426388

QUESTION

I need to deserialize a complex JSON with multiple classes in POJO

Asked 2020-Jun-08 at 18:57

I know I'm doing something wrong, but, am struggling to figure it out. please help.

Jackson Json Conf Camel Blueprint Spring:

...

ANSWER

Answered 2020-Jun-08 at 18:57

This link, article, information has solved my problem and given better understanding on inner classes and Jackson.

Source https://stackoverflow.com/questions/62225368

QUESTION

U-net: TypeError: __call__() missing 1 required positional argument: 'inputs'

Asked 2020-Jan-04 at 13:00

i am working on segmentation of brain tumor dataset provided by BraTS challenge based on u-net. After defining the model at the stage of training an error occurred.

The error is:

...

ANSWER

Answered 2019-Sep-17 at 19:17

Older versions of Keras require you to use 'inputs' instead of 'input' as the name of the first input parameter for Model. Check if you can update your Keras version (current stable is 2.2.5) or try this line:

Source https://stackoverflow.com/questions/57972486

QUESTION

Importing XML to MS Access: Non standard xml?

Asked 2019-Nov-29 at 03:13

I am trying to import an XML file, sourced from: https://www.dsireusa.org/resources/database-archives/ into MS Access.

I have done simple imports CSV imports previously. Upon attempting to import the XML, the import fails completely.

Snooping around, I found that the XML is formatted differently than XMLs I am able to upload successfully. To my understanding, a standard XML looks like this:

...

ANSWER

Answered 2019-Nov-29 at 02:45

The same web site, from the URL you provided, has *.zip files with the *.csv files. The *.csv files have the same content as XML files. So you can easily download *.zip files, unzip them, and load *.csv files into MS Access.

Source https://stackoverflow.com/questions/59097563

QUESTION

Angular 7 Unable to include a custom typescript definition file

Asked 2019-Oct-04 at 10:24

I created a custom typescript definition file (brat.d.ts)

...

ANSWER

Answered 2018-Dec-03 at 07:26

You add declarations in a .d.ts file, and they become globally available in your project. But you'll need to tweak the tsconfig.json firstly, by adding the following:

Source https://stackoverflow.com/questions/53589095

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

Vulnerabilities

No vulnerabilities reported

Install brat

Please follow the following steps, in the order in which they are ordered. Otherwise, results are not guaranteed.
Clone the latest Brat version: git clone git://github.com/presidentbeef/brat.git
Change to new directory: cd brat
Run sh ./build.sh
Optionally, run sudo sh ./install.sh. This will install in /usr by default. Append a directory to change this.
Download the latest
Decompress the archive (unzip brat-master.zip)
Change to the new directory (cd brat-master)
Run sh ./build.sh
Optionally, run sudo sh ./install.sh. This will install in /usr by default. Append a directory to change this.

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 .

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