fepegar/torchio

Medical imaging toolkit for deep learning

torchio's Issues

NormalisationTransform has no attribute masking_method

I get an error with
transfo = Compose(( Rescale(masking_method='mask', verbose=True),))

In the init of NormalizationTransform you use self.masking_method
but it is not assign

Add badges

Add an option to shuffle the queue after filling it

Write functions to switch from NiBabel and SimpleITK without writing to disk

Include all transforms in notebook

Add support for 2D images

Add support for multiple and missing modalities

Add random elastic transform

Add more docs for Queue

Improve label sampler efficiency

Attempting to set a non-orthogonal rotation matrix

This happens sometimes. I need to figure out how to reproduce this error.

Exception thrown in SimpleITK Euler3DTransform_SetMatrix: /tmp/SimpleITK-build/ITK-prefix/include/ITK-4.13/itkRigid3DTransform.hxx:94:
itk::ERROR: Euler3DTransform(0x558bdd7a4780): Attempting to set a non-orthogonal rotation matrix

Should the affine be changed after applying affine transforms?

Add CenterCropOrPad transform

This is useful when images in the dataset have different sizes.

See TensorFlow and PyTorch implementations.

Use better issue templates

Random motion is applied to label image

@romainVala reported this in #24

Add RandomCrop transform

Related to #22

Add exclude/include parameters to transforms kwargs

Use case: loading an MRI and CT from the same patients. We probably want very different transforms for each image, but we still want them to happen in the same parallel process.

Stop modifying input in transforms

Add typing hints

save_sample from ImagesDataset

When using the save_sample method from ImagesDataset
the nifti have a wrong dimention one should change

        tensor = sample[key]['data']

by

        tensor = sample[key]['data'].squeeze()

Not sure if this is the rigth place for this function, why not put it directly in io.py ?

File is lost when overwriting without changes

$ torchio-transform /tmp/t1_ras.nii ToCanonical /tmp/t1_ras.nii 
[1]    2066 bus error (core dumped)  torchio-transform /tmp/t1_ras.nii ToCanonical /tmp/t1_ras.nii

And /tmp/t1_ras.nii gets corrupted.

This is an issue with NiBabel: nipy/nibabel#492

Add Resample transform

Assert that all images in subject list have different names

Possibility to use external mask when masking function

For some Transform : histogram_standardization rescale z_normalization there may be an interest to use a mask (just to compute percentyl or min max values) then the transform is apply to the all images

This is possible with histogram_standardization (and we should add the option with rescale)

My point is that a masking_function is not an easy job, and I do prefer to use mask compute independently (with your prefered software)

In the case of external mask, you can easily use them by including then in the ImageDataset

suj = [[
    Image('T1','/oneT1.nii.gz',INTENSITY),
    Image('mask','/coresponding_mask.nii.gz',LABEL)
     ]]

Then you can use a parameter mask_field_name to get this mask when needed

here is an example of such an implementation
https://github.com/romainVala/torchio/blob/master/torchio/transforms/rescale_within_mask.py

but I thing it is better, to directly incorporate it as an optional feature of the Rescale class with something like

   if sefl.mask_field_name is not None :
       mask_data = sample[self.mask_field_name]['data']

About ZNormalization I would prefer to set use_mean_threshold to False by default and add the possiblity to use either a masking_function or the external mask

For histogram_standardization, a masking_function is expected, (but not use in the call), I added the possibility of external mask
https://github.com/romainVala/torchio/blob/master/torchio/transforms/histogram_standardization.py

of course those option are exclusive, and the user should set only one of them, I am not sure what the best way to code it properly, I did something like

    if masking_function is not None:
        mask = masking_function(img)
    else:
        if mask_data is not None:
            mask = mask_data
        else:
            mask = np.ones_like(img, dtype=np.bool)

Create Image class for ImageDataset

Related to #24

Add Reorient transform

Wrong intensity when RandomMotion is applied after ZNormalization

To reproduce:

from torchio import Image, ImagesDataset, INTENSITY
from torchio.transforms import (
    RandomAffine,
    RandomFlip,
    RandomNoise,
    RandomBiasField,
    RandomElasticDeformation,
    RandomMotion,
    ZNormalization,
)

paths_list = [[
    Image('image', '~/Dropbox/MRI/t1.nii.gz', INTENSITY),
]]

seed = None
verbose = True

transforms = [
    ZNormalization(verbose=verbose),
    RandomMotion(proportion_to_augment=1, seed=seed, verbose=verbose),
    # RandomNoise(seed=seed, verbose=verbose),
    # RandomBiasField(seed=seed, verbose=verbose),
    # RandomFlip(axes=(0,), seed=seed, verbose=verbose),
    # RandomAffine(seed=seed, verbose=verbose),
    # RandomElasticDeformation(proportion_to_augment=0.1, seed=seed, verbose=verbose),
]

dataset = ImagesDataset(paths_list)

sample = dataset[0]
for i, transform in enumerate(transforms):
    transformed = transform(sample)
    name = transform.__class__.__name__
    path = f'/tmp/{i}_{name}.nii.gz'
    dataset.save_sample(transformed, dict(image=path))

@romainVala do you know why this could be? I'm probably missing some theory about the Fourier transform.

Group random parameters in sample dictionary

Add 3D Slicer module

Add Resize transform

Related to #30

Error when patch size and image size are the same in ImageSampler

Reported in #50.

compose augmentation with given probabilitie

I may be a good feature to add, if we can compose augmentation in a similar way as

https://albumentations.readthedocs.io/en/latest/probabilities.html#oneof-block

this make it very modular

write sfrom and qform

I notice that you set (in _write_nifti in io.py)

nii.header['sform_code'] = 0

It is more robust (for other software) to set both sform and qform. I would prefer to have

nii.header['sform_code'] = 1

this will save both sfrom and qform (to the same value)

Apply affine transform to all images simultaneously

Add unit tests

Add visualization utils

Add MRI k-Space Motion Artefact Augmentation

Shaw et al., 2019.

Add __repr__ to all classes

Rescale transform needs an input range

Add support for CUDA FFT and resampling

https://www.idtools.com.au/gpu-accelerated-fft-compatible-numpy/
NifTK/NiftyNet@382ed49

Add bias field transform

errro in random_bias_field.py

Hello
I get the following error when I try to apply the bias_field

/data/romain/toolbox_python/torchio/torchio/transforms/random_bias_field.py in apply_transform(self, sample)
     34             bias_field = self.generate_bias_field_map(
     35                 image_dict['data'], self.order, coefficients)
---> 36             image_dict['data'] *= torch.from_numpy(bias_field)
     37         return sample
     38 

RuntimeError: unsupported operation: more than one element of the written-to tensor refers to a single memory location. Please clone() the tensor before performing the operation.

if I change the corresponding line with

            iii = image_dict['data'] * torch.from_numpy(bias_field)
            image_dict['data'] = iii

it pass,
very strange I do not understand why ...

Label image sampler

Hi fernando,

I recently switched from tf to pytorch and I was really happy to find your library.
Great work! Thanks.

• I added a more efficient image sampler to sample random patches which should contain
  at least one point of a specific label.
  https://github.com/lab-midas/midas-torchio/blob/dev_tobias/torchio/data/sampler/label.py
  (code and examples are still a bit messy, I will work on this the next days).
  But maybe you can use (parts of) it ;)

• There was also a minor issue if the patch size is equal to the image size in a dimension
  (missing +1, rand numbers low=a high=b -> sample from [a,b) so b can be the max_size). I corrected this.
  This is very helpful to use the patch sampler as a slice sampler (for instance slicing 512x512 from 512x512x156 volumes).

Cheers
Tobias

Add docstrings

Add weighted sampler

Add Crop transform

Add antialiasing option to Resample and RandomAffine

As in NifTK/NiftyNet@a91644b#diff-5b79901b7b2f56394aca30c562e9e186

Should ImagesDataset return torch tensors?

Add image padding

It can be useful to pad the images in the transform operations.
In particular, the current grid sampler ignore the borders of the full image, adding a padding of the size of the border could solve this problem (if consistent with training).

understanding the input format

Hi there

Just a small issue in order to fully understand the input format logic
I see in torchio.py that you define 3 data type : Intensity, label and sampling_map
what is the implication of choosing one of those ?

Why in your example_multimodal.py do you define one_subject_dict with a 'label' which has type=torchio.INTENSITY ? (why not torchio.LABEL ?)

many thanks