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cbia
Bio Volumentations
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1be3c659
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1be3c659
authored
1 week ago
by
Lucia D. Hradecka
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update readme and docs
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Make version 1.3.2 default
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@@ -313,7 +313,7 @@ However, you cannot define your own target types, as that would require re-imple
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@@ -313,7 +313,7 @@ However, you cannot define your own target types, as that would require re-imple
### A List of Implemented Transformations
### A List of Implemented Transformations
P
oint transformations:
Intensity-based p
oint transformations:
```
python
```
python
Normalize
Normalize
NormalizeMeanStd
NormalizeMeanStd
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@@ -324,14 +324,14 @@ RandomBrightnessContrast
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@@ -324,14 +324,14 @@ RandomBrightnessContrast
RandomGamma
RandomGamma
```
```
L
ocal transformations:
Intensity-based l
ocal transformations:
```
python
```
python
GaussianBlur
GaussianBlur
RandomGaussianBlur
RandomGaussianBlur
RemoveBackgroundGaussian
RemoveBackgroundGaussian
```
```
Geometric transformations:
Geometric
(spatial)
transformations:
```
python
```
python
AffineTransform
AffineTransform
Resize
Resize
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@@ -347,6 +347,14 @@ RandomFlip
...
@@ -347,6 +347,14 @@ RandomFlip
RandomCrop
RandomCrop
```
```
Other transformations:
```
python
Contiguous
StandardizeDatatype
ConversionToFormat
```
### Runtime
### Runtime
Here, we present the execution times (mean ± standard deviation) of individual transformations from our library
Here, we present the execution times (mean ± standard deviation) of individual transformations from our library
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@@ -133,8 +133,8 @@ images of shape ``[150, 300, 300]``, ``[1, 150, 300, 300]``, as well as ``[4, 15
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@@ -133,8 +133,8 @@ images of shape ``[150, 300, 300]``, ``[1, 150, 300, 300]``, as well as ``[4, 15
If you want to use a multi-channel :class:`mask` or :class:`float_mask`, you have to split it into
If you want to use a multi-channel :class:`mask` or :class:`float_mask`, you have to split it into
a set of single-channel :class:`mask` or :class:`float_mask` targets, respectively, and input them
a set of single-channel :class:`mask` or :class:`float_mask` targets, respectively, and input them
as stand-alone targets (see
as stand-alone targets (see
`the respective section below <https://biovolumentations.readthedocs.io/1.3.1/examples.html#example-transforming-multiple-targets-of-the-same-type>`_
.
`the respective section below <https://biovolumentations.readthedocs.io/1.3.1/examples.html#example-transforming-multiple-targets-of-the-same-type>`_
below
on transforming multiple masks with a single image).
on transforming multiple masks with a single image).
The :class:`keypoints` target is represented as a list of tuples. Each tuple represents
The :class:`keypoints` target is represented as a list of tuples. Each tuple represents
the absolute coordinates of a keypoint in the volume, so it must contain either 3 or 4 numbers
the absolute coordinates of a keypoint in the volume, so it must contain either 3 or 4 numbers
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@@ -148,6 +148,9 @@ as keyword arguments of a call to the :class:`Compose` object. Consequently, the
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@@ -148,6 +148,9 @@ as keyword arguments of a call to the :class:`Compose` object. Consequently, the
dictionary using the same keys. The default key values are :class:`'image'`, :class:`'mask'`, :class:`'float_mask'`,
dictionary using the same keys. The default key values are :class:`'image'`, :class:`'mask'`, :class:`'float_mask'`,
:class:`'keypoints'`, :class:`'bboxes'`, and :class:`'value'`.
:class:`'keypoints'`, :class:`'bboxes'`, and :class:`'value'`.
Prior to applying any user-defined transformation, the :class:`mask` and :class:`float_mask` targets are type-casted to
integer and floating-point datatypes, respectively.
Importantly, there must always be an :class:`image`-type target in the sample.
Importantly, there must always be an :class:`image`-type target in the sample.
You cannot define your own target types; that would require re-implementing all existing transforms.
You cannot define your own target types; that would require re-implementing all existing transforms.
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