split_dataset | minimal package for saving and reading large HDF5 | Data Manipulation library
kandi X-RAY | split_dataset Summary
kandi X-RAY | split_dataset Summary
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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Top functions reviewed by kandi - BETA
- 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
split_dataset Key Features
split_dataset Examples and Code Snippets
Community Discussions
Trending Discussions on split_dataset
QUESTION
I am running cross validation on dataset and getting
...ANSWER
Answered 2021-Nov-20 at 22:36Testing my remove
hypothesis
QUESTION
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 15:46In 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 :- you'll initialize the data(like you do in any C program)
- Create a buffer object using clCreateBuffer() (think of it as reserving memory on the device) (similarly allocate for output)
- Send the initialized data to the device using clEnqueueWriteBuffer()(to the earlier reserved space)
- Invoke the kernel using clEnqueueNDRangeKernel()(now the device has kernel code and data)
- Execute the kernel code
- Write the output data to reserved space by host
- 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)
QUESTION
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 13:20According to the documentation, in Keras, model.predict() expects a numpy array. So try this:
QUESTION
I'm trying to create and train a Sequential model like so:
...ANSWER
Answered 2021-Jul-28 at 18:49BinaryCrossentropy
is imported from tf.keras.metrics
hence gradients could not be computed.
Correct import should have been from tensorflow.keras.losses import BinaryCrossentropy
.
QUESTION
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 13:41The 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 :
QUESTION
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 21:12What you miss is that the shape of y_test
.
QUESTION
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 16:15I 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:
QUESTION
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 14:50Solved: 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
QUESTION
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 07:38in 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.
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Install split_dataset
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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