#### NOTE
New to DeepInverse? Get started with the basics with the
[5 minute quickstart tutorial](https://deepinv.org/auto_examples/basics/demo_quickstart.html.md#sphx-glr-auto-examples-basics-demo-quickstart-py)..
# Loading scientific images
This example presents the various input/output functions provided by DeepInverse
for handling medical and scientific imaging formats. We demonstrate loading and
plotting from DICOM, NIfTI, ISMRMRD, PyTorch, NumPy and raster data sources.
```Python
import deepinv as dinv
```
## 1. Load DICOM
DICOM files are commonly used in clinical imaging. We can fetch and load them
directly using [`deepinv.utils.load_dicom()`](https://deepinv.org/api/stubs/deepinv.utils.load_dicom.html.md#deepinv.utils.load_dicom). Here, we demonstrate on a
demo DICOM from the Internet.
This function requires `pydicom`. Install it with `pip install pydicom`.
#### NOTE
You can also call the `io` functions directly as `dinv.io.load_...`
```Python
x = dinv.utils.io.load_dicom(
dinv.utils.io.load_url(
"https://github.com/robyoung/dicom-test-files/raw/refs/heads/master/data/pydicom/693_J2KI.dcm"
)
) # (1,H,W)
dinv.utils.plot({"dicom": x.unsqueeze(0)})
```
## 2. Load NIfTI
NIfTI files are often used for volumetric neuroimaging data. We load them using [`deepinv.utils.load_nifti()`](https://deepinv.org/api/stubs/deepinv.utils.load_nifti.html.md#deepinv.utils.load_nifti).
Since `nibabel` doesn’t support file buffers, we download a sample volume first.
This function requires `nibabel`. Install it with `pip install nibabel`.
```Python
import requests
save_path = dinv.utils.get_cache_home() / "tmp.nii.gz"
with open(save_path, "wb") as f:
f.write(
requests.get(
"https://github.com/neurolabusc/niivue-images/raw/refs/heads/main/Iguana.nii.gz"
).content
)
x = dinv.utils.io.load_nifti(save_path).unsqueeze(0) # (1, H, W, D)
x = x[..., x.shape[-1] // 2] # take central slice, (1,H,W)
dinv.utils.plot({"nifti slice": x.unsqueeze(0)})
```
## 3. Load ISMRMRD
ISMRMRD is a standard raw MRI k-space format. We load a k-space slice using [`deepinv.utils.load_ismrmd()`](https://deepinv.org/api/stubs/deepinv.utils.load_ismrmd.html.md#deepinv.utils.load_ismrmd)
and compute a root-sum-of-squares reconstruction.
```Python
y = dinv.utils.io.load_ismrmd(
dinv.utils.io.load_url(
dinv.utils.demo.get_image_url("demo_fastmri_brain_multicoil.h5")
),
data_name="kspace",
data_slice=0,
) # (2,N,H,W) where N is coils
rss = dinv.physics.MultiCoilMRI(img_size=y.shape[-2:]).A_adjoint(
y.unsqueeze(0), rss=True
) # (1,2,H,W)
dinv.utils.plot({"ismrmrd rss": rss})
```
## 4. Load tensors and arrays
We provide helper functions for loading tensors and arrays directly, for example provided
in the `DeepInverse HuggingFace demo repository `.
```Python
x = dinv.utils.io.load_torch(
dinv.utils.load_url(dinv.utils.demo.get_image_url("CT100_256x256_0.pt"))
) # (1,1,H,W)
y = dinv.utils.io.load_np(
dinv.utils.load_url(
dinv.utils.demo.get_image_url("brainweb_t1_ICBM_1mm_subject_0_slice_0.npy")
)
) # (H,W)
dinv.utils.plot({"torch": x, "numpy": y.unsqueeze(0).unsqueeze(0)})
```
## 6. Load raster images
Raster formats (e.g. GeoTIFF, COSAR) can be streamed with patches.
See [`deepinv.utils.load_raster()`](https://deepinv.org/api/stubs/deepinv.utils.load_raster.html.md#deepinv.utils.load_raster) for patch options.
This function requires `rasterio`. Install it with `pip install rasterio`.
```Python
patches = dinv.utils.io.load_raster(
dinv.utils.io.load_url(
"https://download.osgeo.org/geotiff/samples/spot/chicago/SP27GTIF.TIF"
),
patch=500,
patch_start=(200, 200),
)
x = next(patches) # Stream patch
dinv.utils.plot({"raster": x.unsqueeze(0)})
```
**Total running time of the script:** (0 minutes 2.527 seconds)
🏷 Tags: MRI
[`Download Jupyter notebook: demo_io.ipynb`](https://deepinv.org/auto_examples/external-libraries/_downloads/a32bd0a614a335662a6e25047fd71948/demo_io.ipynb)
[`Download Python source code: demo_io.py`](https://deepinv.org/auto_examples/external-libraries/_downloads/a54a55f65de048c35531aa4136f15d94/demo_io.py)
[`Download zipped: demo_io.zip`](https://deepinv.org/auto_examples/external-libraries/_downloads/000ccef617fdcd3beaaa11d5f96a4423/demo_io.zip)
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