unet | U-Net Biomedical Image Segmentation | Machine Learning library
kandi X-RAY | unet Summary
kandi X-RAY | unet Summary
U-Net Biomedical Image Segmentation
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QUESTION
I have 10000119~10000130 patient 3D ct images I've sliced 3D CT images into 250 slices for each patient data along the z axis.
I want to sort this data path in numerical order for each slice for each patient. What I want to do is the following:
...ANSWER
Answered 2022-Mar-17 at 05:31I found my own answer..! I hope this will help other deeplearning engineer too! I hope you have a great day! I explicitly coded to get the intuition at hand.
QUESTION
I've been experimenting with a part of MIDV 500 dataset, tried to localize document quadrilateral. So, my output is a vector of 8 floats.
RGB images were scaled to 960 by 540 pixels (960, 540, 3), pixel values were scaled to [0..1]. Target vector also scaled to [0..1] (simply divided by image dims)
My first approach was pretrained CNN (+ fine-tuning) from Keras applications (tried EfficientNetB0-2) with following Dense head:
...ANSWER
Answered 2022-Mar-10 at 13:59Two things:
- Please check which version of TensorFlow (TF) you are using. I believe that from 2.5, you don't need to rescale the input image to the range [0-1]. The network expects tensors from [0-255]. https://keras.io/api/applications/efficientnet/
- Your model architecture and callbacks look all right (I am not an expert on this optimizer + loss though). Thus, I am assuming that the problem might come from your data input. Are you using ImageDataGenerator as input and for splitting the data from training and validation? If not, it might be worth a try. You can specify your validation subset and the generator will split the data for you. More info here: https://www.tensorflow.org/api_docs/python/tf/keras/preprocessing/image/ImageDataGenerator
QUESTION
I am training a Unet segmentation model for binary class. The dataset is loaded in tensorflow data pipeline. The images are in (512, 512, 3) shape, masks are in (512, 512, 1) shape. The model expects the input in (512, 512, 3) shape. But I am getting the following error. Input 0 of layer "model" is incompatible with the layer: expected shape=(None, 512, 512, 3), found shape=(512, 512, 3)
Here are the images in metadata dataframe.
Randomly sampling the indices to select the training and validation set
...ANSWER
Answered 2022-Mar-08 at 13:38Use train_batches
in model.fit
and not train_images
. Also, you do not need to use repeat()
, which causes an infinite dataset if you do not specify how many times you want to repeat your dataset. Regarding your labels error, try rewriting your model like this:
QUESTION
I’m now writing my own network with Pytorch. And I want to use a pretrained model in my net. Here is my overwriting init() code:
...ANSWER
Answered 2022-Mar-04 at 09:15For the basic layers (e.g., nn.Conv
, nn.Linear
, etc.) the parameters are initialized by the __init__
method of the layer.
For example, look at the source code of class _ConvNd(Module)
(the class from which all other convolution layers are derived). At the bottom of its __init__
it calls self.reset_parameters()
which initialize the weights.
Therefore, if your nn.Module
does not have any "independent" nn.Parameter
s, only trainable parameters inside sub-nn.Module
s, when you construct your network, all weights of the sub modules are being initialized as the sub modules are constructed.
That is, once you call h_model = H_model()
the weights of h_model
are already initialized to their default values. Calling h_model.load_state_dict(...)
overrides these values to the desired pre-trained weights.
QUESTION
Is there a way that we can write a custom AT command for unetstack/subnero modems ? I refered Chapter 12 but could not find this information.
...ANSWER
Answered 2022-Feb-26 at 19:33AT command shells (and Groovy shells) can be extended with shell extensions. Shell extensions implement a org.arl.fjage.shell.ShellExtension
tag interface. Static methods (and attributes) of the shell extension class are made available in the shell as commands (and variables/constants). In the AT command shell, they are called using AT commands as briefly described in section 12.3 of the Unet handbook.
For example, the handbook shows an example of loading the PhysicalShellExt
via:
QUESTION
I am trying to learn build a U-NET architecture from scratch. I have written this code but the problem is that when I try to run to check the output of the encoder part, I am having issues with it. When you the run the code below , you'll get
...ANSWER
Answered 2022-Feb-23 at 08:54There was a code logic mistake in the forward
of Encoder
I did:
QUESTION
I use unet for image segmentation my question is what does below code mean
...ANSWER
Answered 2022-Jan-18 at 19:36About first question test_img_norm=test_img[:,:,0][:,:,None]
, test_img[:,:,0]
will copy first channel of image and test_img[:,:,0][:,:,None]
will add one channel to it. for example if you have an image with shape (256, 256, 3)
, test_img_norm
shape will be (256, 256, 1)
.
About second part of question, model.predict(test_img_other_input)[0,:,:,0] > 0.2
will give you a boolean array. For every element in output of UNet, if element is less than 0.2, output would be True
, otherwise would be False
. And finally .astype(np.uint8)
make booleans to zero or one.
QUESTION
I would like to implement Dice Lose like this from dice_loss_for_keras.py:
...ANSWER
Answered 2022-Jan-13 at 08:15You need to convert y_true
to 1-hot representation in order to apply per-class dice loss.
It seems like you have tf.one_hot
function that does it for you.
Once you have y_true
in the same shape as y_pred
, you can use your code to compute the dice score for each class separately, and then combine the scores of all classes to get the final scalar loss.
QUESTION
I wrote a tfrecord file and fed in my Unet model but got a problem with the input shape. Below is my code.
About the data:
- 484 training images, each has a shape of (240, 240, 155, 4), these 4 numbers are the height, width, number of layers and channels respectively.
- 484 labels, each has a shape of (240, 240, 155)
I used the first 2 examples:
...ANSWER
Answered 2021-Nov-29 at 16:49Your model expects the shape (samples, 240, 240, 155, 4)
, so try something like this:
QUESTION
I'm trying to implement the UNET at the keras website:
Image segmentation with a U-Net-like architecture
With only one change. use Dice loss instead of "sparse_categorical_crossentropy". However, every time I try something, I get different error. I'm coding on google colab using Tensorflow 2.7.
For example, I tried using
...ANSWER
Answered 2021-Dec-31 at 10:24You are passing 1-dimensional vectors to K.dot
, while the ValueError is saying that K.dot
requires arrays with 2-dimensions.
You can replace it with element-wise multiplication, i.e. intersection = K.sum(targets *inputs)
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