Data input and output
Dealing with volumetric data can be done by qim3d
for the most common image formats available.
Currently, it is possible to directly load tiff
, h5
, nii
,txm
, vol
and common PIL
formats using one single function.
qim3d.io
qim3d.io.Downloader
Class for downloading large data files available on the QIM data repository.
Attributes:
Name | Type | Description |
---|---|---|
folder_name |
str
|
Folder class with the name of the folder in https://data.qim.dk/ |
Syntax for downloading and loading a file is qim3d.io.Downloader().{folder_name}.{file_name}(load_file=True)
Overview of available data
Below is a table of the available folders and files on the QIM data repository.
Folder name | File name | File size |
---|---|---|
Coal |
CoalBrikett CoalBrikett_Zoom CoalBrikettZoom_DOWNSAMPLED |
2.23 GB 3.72 GB 238 MB |
Corals |
Coral_1 Coral_2 Coral2_DOWNSAMPLED MexCoral |
2.26 GB 2.38 GB 162 MB 2.23 GB |
Cowry_Shell |
Cowry_Shell Cowry_DOWNSAMPLED |
1.82 GB 116 MB |
Crab |
HerrmitCrab OkinawaCrab |
2.38 GB 1.86 GB |
Deer_Mandible |
Animal_Mandible DeerMandible_DOWNSAMPLED |
2.79 GB 638 MB |
Foam |
Foam Foam_DOWNSAMPLED Foam_2 Foam_2_zoom |
3.72 GB 238 MB 3.72 GB 3.72 GB |
Hourglass |
Hourglass Hourglass_4X_80kV_Air_9s_1_97um Hourglass_longexp_rerun |
3.72 GB 1.83 GB 3.72 GB |
Kiwi |
Kiwi |
2.86 GB |
Loofah |
Loofah Loofah_DOWNSAMPLED |
2.23 GB 143 MB |
Marine_Gastropods |
MarineGatropod_1 MarineGastropod1_DOWNSAMPLED MarineGatropod_2 MarineGastropod2_DOWNSAMPLED |
2.23 GB 143 MB 2.60 GB 166 MB |
Mussel |
ClosedMussel1 ClosedMussel1_DOWNSAMPLED |
2.23 GB 143 MB |
Oak_Branch |
Oak_branch OakBranch_DOWNSAMPLED |
2.38 GB 152 MB |
Okinawa_Forams |
Okinawa_Foram_1 Okinawa_Foram_2 |
1.84 GB 1.84 GB |
Physalis |
Physalis Physalis_DOWNSAMPLED |
3.72 GB 238 MB |
Raspberry |
Raspberry2 Raspberry2_DOWNSAMPLED |
2.97 GB 190 MB |
Rope |
FibreRope1 FibreRope1_DOWNSAMPLED |
1.82 GB 686 MB |
Sea_Urchin |
SeaUrchin Cordatum_Shell Cordatum_Spine |
2.60 GB 1.85 GB 183 MB |
Snail |
Escargot |
2.60 GB |
Sponge |
Sponge |
1.11 GB |
Example
Source code in qim3d/io/downloader.py
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|
qim3d.io.load
load(path, virtual_stack=False, dataset_name=None, return_metadata=False, contains=None, progress_bar=True, force_load=False, dim_order=(2, 1, 0), **kwargs)
Load data from the specified file or directory.
Supported formats:
Tiff
(including file stacks)HDF5
TXRM
/TXM
/XRM
NIfTI
PIL
(including file stacks)VOL
/VGI
DICOM
Parameters:
Name | Type | Description | Default |
---|---|---|---|
path |
str or PathLike
|
The path to the file or directory. |
required |
virtual_stack |
bool
|
Specifies whether to use virtual stack when loading files. Default is False. |
False
|
dataset_name |
str
|
Specifies the name of the dataset to be loaded in case multiple dataset exist within the same file. Default is None (only for HDF5 files) |
None
|
return_metadata |
bool
|
Specifies whether to return metadata or not. Default is False (only for HDF5 and TXRM/TXM/XRM files) |
False
|
contains |
str
|
Specifies a part of the name that is common for the TIFF file stack to be loaded (only for TIFF stacks). Default is None. |
None
|
progress_bar |
bool
|
Displays tqdm progress bar. Useful for large files. So far works only for linux. Default is False. |
True
|
force_load |
bool
|
If the file size exceeds available memory, a MemoryError is raised. If force_load is True, the error is changed to warning and the loader tries to load it anyway. Default is False. |
False
|
dim_order |
tuple
|
The order of the dimensions in the volume for .vol files. Default is (2,1,0) which corresponds to (z,y,x) |
(2, 1, 0)
|
**kwargs |
Additional keyword arguments to be passed |
{}
|
Returns:
Name | Type | Description |
---|---|---|
vol |
(ndarray, memmap, Dataset, ArrayProxy or tuple)
|
The loaded volume If |
Raises:
Type | Description |
---|---|
MemoryError
|
if the given file size exceeds available memory |
Source code in qim3d/io/loading.py
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|
qim3d.io.load_mesh
Load a mesh from an .obj file using trimesh.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
filename |
The path to the .obj file. |
required |
Returns:
Name | Type | Description |
---|---|---|
mesh |
A trimesh object containing the mesh data (vertices and faces). |
Source code in qim3d/io/loading.py
qim3d.io.save
save(path, data, replace=False, compression=False, basename=None, sliced_dim=0, chunk_shape='auto', **kwargs)
Save data to a specified file path.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
path |
str
|
The path to save file to |
required |
data |
ndarray
|
The data to be saved |
required |
replace |
bool
|
Specifies if an existing file with identical path should be replaced. Default is False. |
False
|
compression |
bool
|
Specifies if the file should be saved with Deflate compression (lossless). Default is False. |
False
|
basename |
str
|
Specifies the basename for a TIFF stack saved as several files (only relevant for TIFF stacks). Default is None |
None
|
sliced_dim |
int
|
Specifies the dimension that is sliced in case a TIFF stack is saved as several files (only relevant for TIFF stacks). Default is 0, i.e., the first dimension. |
0
|
**kwargs |
Additional keyword arguments to be passed to the DataSaver constructor |
{}
|
Example
import qim3d
# Generate synthetic blob
synthetic_blob = qim3d.generate.blob(noise_scale = 0.015)
qim3d.io.save("blob.tif", synthetic_blob, replace=True)
Volumes can also be saved with one file per slice:
Source code in qim3d/io/saving.py
qim3d.io.save_mesh
Save a trimesh object to an .obj file.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
filename |
The name of the file to save the mesh. |
required | |
mesh |
A trimesh.Trimesh object representing the mesh. |
required |
Example
Source code in qim3d/io/saving.py
qim3d.io.export_ome_zarr
export_ome_zarr(path, data, chunk_size=256, downsample_rate=2, order=1, replace=False, method='scaleZYX', progress_bar=True, progress_bar_repeat_time='auto')
Export 3D image data to OME-Zarr format with pyramidal downsampling.
This function generates a multi-scale OME-Zarr representation of the input data, which is commonly used for large imaging datasets. The downsampled scales are calculated such that the smallest scale fits within the specified chunk_size
.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
path |
str
|
The directory where the OME-Zarr data will be stored. |
required |
data |
ndarray or array
|
The 3D image data to be exported. Supports both NumPy and Dask arrays. |
required |
chunk_size |
int
|
The size of the chunks for storing data. This affects both the original data and the downsampled scales. Defaults to 256. |
256
|
downsample_rate |
int
|
The factor by which to downsample the data for each scale. Must be greater than 1. Defaults to 2. |
2
|
order |
int
|
The interpolation order to use when downsampling. Defaults to 1 (linear). Use 0 for a faster nearest-neighbor interpolation. |
1
|
replace |
bool
|
Whether to replace the existing directory if it already exists. Defaults to False. |
False
|
method |
str
|
The method used for downsampling. If set to "dask", Dask arrays are used for chunking and downsampling. Defaults to "scaleZYX". |
'scaleZYX'
|
progress_bar |
bool
|
Whether to display a progress bar during export. Defaults to True. |
True
|
progress_bar_repeat_time |
str or int
|
The repeat interval (in seconds) for updating the progress bar. Defaults to "auto". |
'auto'
|
Raises:
Type | Description |
---|---|
ValueError
|
If the directory already exists and |
ValueError
|
If |
Example
Returns:
Name | Type | Description |
---|---|---|
None |
This function writes the OME-Zarr data to the specified directory and does not return any value. |
Source code in qim3d/io/ome_zarr.py
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|
qim3d.io.import_ome_zarr
Import image data from an OME-Zarr file.
This function reads OME-Zarr formatted volumetric image data and returns the specified scale. The image data can be lazily loaded (as Dask arrays) or fully computed into memory.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
path |
str
|
The file path to the OME-Zarr data. |
required |
scale |
int or str
|
The scale level to load. If 'highest', loads the finest scale (scale 0). If 'lowest', loads the coarsest scale (last available scale). Defaults to 0. |
0
|
load |
bool
|
Whether to compute the selected scale into memory. If False, returns a lazy Dask array. Defaults to True. |
True
|
Returns:
Type | Description |
---|---|
np.ndarray or dask.array.Array: The requested image data, either as a NumPy array if |
|
or a Dask array if |
Raises:
Type | Description |
---|---|
ValueError
|
If the requested |