gradient_decode_dicom
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🏨Gradient Health DICOM operation for Tensorflow
Gradient Decode Dicom Tensorflow Operation
Getting started
-
Install the DCMTK toolkit
sudo apt-get install libdcmtk-dev
-
Install gradient_decode_dicom
pip3 install gradient-decode-dicom
Documentation
The gradient_decode_dicom
package has two operations, decode_dicom_image
which decodes the pixel data from DICOM files, and decode_dicom_data
which decodes tag information. tags
contains useful DICOM tags such as tags.PatientsName
. We borrow the same tag notation from the pydicom
dicom package.
Getting DICOM Image Data
gradient_decode_dicom.decode_dicom_image(
contents,
color_dim=False,
on_error='skip',
scale='preserve'
dtype=tf.uint16
name=None
)
-
contents
: A Tensor of type string. 0-D. The byte string encoded DICOM file -
color_dim
: An optionalbool
. Defaults toFalse
. IfTrue
, a third channel will be appended to all images forming a 3-D tensor. A 1024 x 1024 grayscale image will be 1024 x 1024 x 1 -
on_error
: Defaults toskip
. This attribute establishes the behavior in case an error occurs on opening the image or if the output type cannot accomodate all the possible input values. For example if the user sets the output dtype to tf.uint8, but a dicom image stores a tf.uint16 type.strict
throws an error.skip
returns a 1-D empty tensor.lossy
continues with the operation scaling the value via thescale
attribute. -
scale
: Defaults topreserve
. This attribute establishes what to do with the scale of the input values.auto
will autoscale the input values, if the output type is integer,auto
will use the maximum output scale for example auint8
which stores values from [0, 255] can be linearly stretched to fill auint16
that is [0,65535]. If the output is float,auto
will scale to [0,1].preserve
keeps the values as they are, an input value greater than the maximum possible output will be clipped. -
dtype
: An optionaltf.DType
from:tf.uint8, tf.uint16, tf.uint32, tf.uint64, tf.float16, tf.float32, tf.float64
. Defaults totf.uint16
. -
name
: A name for the operation (optional).
Returns
A Tensor
of type dtype
and the shape is determined by the DICOM file.
Getting DICOM Tag Data
gradient_decode_dicom.decode_dicom_data(
contents,
tags=None,
name=None
)
-
contents
: A Tensor of type string. 0-D. The byte string encoded DICOM file -
tags
: A Tensor of typetf.uint32
of any dimension. Theseuint32
numbers map directly to DICOM tags -
name
: A name for the operation (optional).
Returns
A Tensor
of type tf.string
and same shape as tags
. If a dicom tag is a list of strings, they are combined into one string and seperated by a double backslash \\
. There is a bug in DCMTK if the tag is a list of numbers, only the zeroth element will be returned as a string.