split_dataset | minimal package for saving and reading large HDF5 | Data Manipulation library

 by   portugueslab Python Version: Current License: Non-SPDX

kandi X-RAY | split_dataset Summary

kandi X-RAY | split_dataset Summary

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

A minimal package for saving and reading large HDF5-based chunked arrays. This package has been developed in the Portugues lab for volumetric calcium imaging data. split_dataset is extensively used in the calcium imaging analysis package fimpy; The microscope control libraries sashimi and brunoise save files as split datasets. napari-split-dataset support the visualization of SplitDatasets in napari.
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              split_dataset has a low active ecosystem.
              It has 13 star(s) with 0 fork(s). There are 4 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 1 open issues and 2 have been closed. On average issues are closed in 298 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of split_dataset is current.

            kandi-Quality Quality

              split_dataset has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              split_dataset has a Non-SPDX License.
              Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

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              split_dataset 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 are not available. Examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed split_dataset and discovered the below as its top functions. This is intended to give you an instant insight into split_dataset implemented functionality, and help decide if they suit your requirements.
            • Applies a crop to the dataset
            • Serializes this Splitter into a dictionary
            • Return a new SplitDataset
            • Saves metadata to file
            • Return an iterator over the slices in this block
            • Crop the current image
            • Update the block structure
            • Update the dimensions of the stack
            • Returns the indices of adjacent blocks
            • Convert a linear index to cartesian coordinates
            • Set the full shape of the stack
            • Set the padding of the block
            • Set the block shape
            Get all kandi verified functions for this library.

            split_dataset Key Features

            No Key Features are available at this moment for split_dataset.

            split_dataset Examples and Code Snippets

            No Code Snippets are available at this moment for split_dataset.

            Community Discussions

            QUESTION

            The truth value of an array with more than one element is ambiguous error?
            Asked 2021-Nov-20 at 22:36

            I am running cross validation on dataset and getting

            ...

            ANSWER

            Answered 2021-Nov-20 at 22:36

            Testing my remove hypothesis

            Source https://stackoverflow.com/questions/70048308

            QUESTION

            How to read a .csv file in OpenCL
            Asked 2021-Sep-01 at 15:46

            I have written the host code in OpenCL. But I need first to read data from a .csv file. I need to make sure that what I did in reading the file is correct. (I am not sure if this is the way of reding a file in opencl)

            1- I put the read file function which is written in c++ before the main .

            2 - then, I put function to mix the data. Also before the main

            3- In the main function, I call the above two function to read the data and then mix it.

            4- then I write the part of host code which include(platform, device, context, queue, buffers....etc)

            This is my code:

            ...

            ANSWER

            Answered 2021-Sep-01 at 15:46

            In short, the OpenCL programming model contains two codes, host code(.c/.cpp..) which runs on host(CPU) and kernel code(.cl) which runs on device(eg:GPU..).

            Host Side :
            1. you'll initialize the data(like you do in any C program)
            2. Create a buffer object using clCreateBuffer() (think of it as reserving memory on the device) (similarly allocate for output)
            3. Send the initialized data to the device using clEnqueueWriteBuffer()(to the earlier reserved space)
            4. Invoke the kernel using clEnqueueNDRangeKernel()(now the device has kernel code and data)
            Device Side:
            1. Execute the kernel code
            2. Write the output data to reserved space by host
            Host Side:
            1. Afer device completes its execution host reads the data from the Device using clEnqueueReadBuffer().

            With this flow, you've offloaded the computation to the device and read the output to host.

            NOTE:

            This explanation is not 100% accurate, I tried to explain it in a simpler manner. I would suggest you read chapter-3 from (https://www.khronos.org/registry/OpenCL/specs/opencl-1.2.pdf)

            Source https://stackoverflow.com/questions/69014171

            QUESTION

            Error when inputting array of outside data into TensorFlow model.predict()
            Asked 2021-Aug-13 at 14:10

            We successfully trained a TensorFlow model based on five climate features and one binary (0 or 1) label. We want an output for an outside input of five new climate variable values that will be inputted into model.predict(). However, we got an error when we tried to input an array of five values. Thanks in advance!

            ...

            ANSWER

            Answered 2021-Aug-11 at 13:20

            According to the documentation, in Keras, model.predict() expects a numpy array. So try this:

            Source https://stackoverflow.com/questions/68736258

            QUESTION

            "No gradients provided for any variable" when trying to fit Keras Sequential
            Asked 2021-Jul-30 at 02:11

            I'm trying to create and train a Sequential model like so:

            ...

            ANSWER

            Answered 2021-Jul-28 at 18:49

            BinaryCrossentropy is imported from tf.keras.metrics hence gradients could not be computed.

            Correct import should have been from tensorflow.keras.losses import BinaryCrossentropy.

            Source https://stackoverflow.com/questions/68529435

            QUESTION

            Divide dataset into 30
            Asked 2021-May-13 at 13:41

            I'm writing a model that I want to use to predict 30 days ahead. My problem is that I need to split the dataset into 30 chunks and when trying I get the error "array split does not result in an equal division".

            Of course, this literally tells me the problem. So yes, I know the problem. My problem is that I can't figure out how to do an equal split. I've tried several different ways to calculate and split it and all end up with this error. I'm not certain where I'm doing wrong so I presume I haven't understood the problem. I'd like some help with this, wouldn't mind a good explanation so I understand it better too.

            This is the split function:

            ...

            ANSWER

            Answered 2021-May-13 at 13:41

            The issue you have is probably that len(train)/30 is not an integer.

            Let's take an example, if you have the following array a = [1, 2, 3, 4, 5], its length is 5. You cannot make it into 2 chunks as len(a)/2 is not an integer.

            If you want to do it despite that, you have to remove parts of the array, or add neutral value. This is a design decision that you must make and that the split function of numpy cannot do for you.

            So let's suppose you accept to lose the last data, meaning that the array [1, 2, 3, 4, 5] will be transformed into [[1, 2], [3, 4]], and the 5 is lost.

            you can do this using the following snippet :

            Source https://stackoverflow.com/questions/67519688

            QUESTION

            Why does tensorflow show inaccurate loss?
            Asked 2021-Mar-31 at 21:12

            I'm using Tensorflow to train a network to predict the third item in a list of numbers.

            When I train, the network appears to train quite well and do well on both the training and test set. However, when I evaluate its performance myself, it seems to be doing quite poorly.

            For example, at the end of training, Tensorflow says that the validation loss is 2.1 x 10^(-5). However, when I compute it myself, I get 0.17 x 10^0. What am I doing wrong?

            Here's code that can be run on Google Colab:

            ...

            ANSWER

            Answered 2021-Mar-31 at 21:12

            What you miss is that the shape of y_test.

            Source https://stackoverflow.com/questions/66893949

            QUESTION

            R targets multiple file outputs
            Asked 2021-Mar-30 at 16:15

            I am looking into using R's targets but I am struggling to have it accept multiple file outputs.

            For example, I want to be able to take a dataset, create a train/test split and write each dataset to a separate file.

            An MWE would be

            _targets.R

            ...

            ANSWER

            Answered 2021-Mar-30 at 16:15

            I recommend appending idx as a column to data and then filtering on it later for the train and test targets. Also, you do not need format = "file" to be able to access datasets later. You can use tar_read() or tar_load() for that. Sketch:

            Source https://stackoverflow.com/questions/66871715

            QUESTION

            Premature end of training in TF OD 2 API
            Asked 2020-Aug-14 at 14:50

            I've been playing with the Tensorflow Object Detection API 2(TF OD 2) in these days, I'm using the git head commit ce3b7227. My aim is to find the most suitable model for my custom dataset, by using the existent DL Architecture present in theTensorFlow 2 Model Zoo. I've generated my TF Records with the following tutorial of Roboflow and I have been training it with my Laptop and Google Colab, in GPU Mode.

            I've found this amazing Roboflow's Colab Notebook, while I've tried to reproduce the same steps with my dataset, by using the models/research/object_detection/model_main_tf2.py, unluckly for me, the training script always ends before it started to iterate. It didn't show any Python Error and also it show some warnings as usual. The complete output is in my Colab Notebook

            I'm fine-tuning the model with the following commands.

            ...

            ANSWER

            Answered 2020-Aug-14 at 14:50

            Solved: For models such as efficientdet_d1_coco17_tpu-32 just change in the pipeline.config the parameter from fine_tune_checkpoint_type: "classification" to fine_tune_checkpoint_type: "detection", check TF Github

            Source https://stackoverflow.com/questions/63362209

            QUESTION

            Tensorflow 2.0 Conv3D input_shape Problem
            Asked 2020-Apr-23 at 07:38

            I' trying to train a CNN on video sequences. My input_data has the shape (5874, 1, 10, 128, 128) which represent (n_samples, channels, frames, height , width). The error is either 4 dimensions are given but 5 expected or 6 dimensions were given. What is the correct way to manage Conv3D?

            setting Input((1,10,128,128)) results to: ValueError: Error when checking input: expected input_1 to have 5 dimensions, but got array with shape (1, 128, 128, 10). but the error is generated after fitting.

            setting Input((1,1,10,128,128)) results to:ValueError: Input 0 of layer conv3d_6 is incompatible with the layer: expected ndim=5, found ndim=6. Full shape received: [None, 1, 1, 128, 128, 10] after executing the model (before fitting)

            I already went through all possible documentation and forums and found nothing. Any tips would be helpful.

            ...

            ANSWER

            Answered 2020-Apr-23 at 07:38

            in the model Tensorflow adds a dimension at the beginning of the data for iteration. So the Input should get only the last four dimensions. But the fit needs 5. after using Dataset.from_tensor_slices, dataset.batch must be used otherwise there is an error while fitting.

            Source https://stackoverflow.com/questions/61341985

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

            Vulnerabilities

            No vulnerabilities reported

            Install split_dataset

            You can install using 'pip install split_dataset' or download it from GitHub, PyPI.
            You can use split_dataset 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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