sparktk.dicom.constructors.import_dcm module
# vim: set encoding=utf-8
# Copyright (c) 2016 Intel Corporation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
from sparktk.tkcontext import TkContext
def import_dcm(dicom_dir_path, tc=TkContext.implicit):
"""
Creates a dicom object with metadataFrame and pixeldataFrame from a dcm file(s)
Parameters
----------
:param dicom_dir_path: (str) Local/HDFS path of the dcm file(s)
:return: (Dicom) returns a dicom object with metadata and pixeldata frames
Examples
--------
#Path can be local/hdfs to dcm file(s)
>>> dicom_path = "../datasets/dicom_uncompressed"
#use import_dcm available inside dicom module to create a dicom object from given dicom_path
>>> dicom = tc.dicom.import_dcm(dicom_path)
#Type of dicom object created
>>> type(dicom)
#Inspect metadata property to see dicom metadata xml content
>>> dicom.metadata.inspect(truncate=30)
[#] id metadata
=======================================
[0] 0 >> pixeldata = dicom.pixeldata.take(1)
>>> pixeldata
[[0L, array([[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 7., 5., ..., 5., 7., 8.],
[ 0., 7., 6., ..., 5., 6., 7.],
...,
[ 0., 6., 7., ..., 5., 5., 6.],
[ 0., 2., 5., ..., 5., 5., 4.],
[ 1., 1., 3., ..., 1., 1., 0.]])]]
"""
if not isinstance(dicom_dir_path, basestring):
raise ValueError("dicom_dir_path parameter must be a string, but is {0}.".format(type(dicom_dir_path)))
TkContext.validate(tc)
scala_dicom = tc.sc._jvm.org.trustedanalytics.sparktk.dicom.internal.constructors.Import.importDcm(tc.jutils.get_scala_sc(), dicom_dir_path)
from sparktk.dicom.dicom import Dicom
return Dicom._from_scala(tc, scala_dicom)
Functions
def import_dcm(
dicom_dir_path, tc=<class 'sparktk.arguments.implicit'>)
Creates a dicom object with metadataFrame and pixeldataFrame from a dcm file(s)
Parameters:
dicom_dir_path | (str): | Local/HDFS path of the dcm file(s) |
Returns | (Dicom): | returns a dicom object with metadata and pixeldata frames |
Examples:
#Path can be local/hdfs to dcm file(s)
>>> dicom_path = "../datasets/dicom_uncompressed"
#use import_dcm available inside dicom module to create a dicom object from given dicom_path
>>> dicom = tc.dicom.import_dcm(dicom_path)
#Type of dicom object created
>>> type(dicom)
<class 'sparktk.dicom.dicom.Dicom'>
#Inspect metadata property to see dicom metadata xml content
>>> dicom.metadata.inspect(truncate=30)
[#] id metadata
=======================================
[0] 0 <?xml version="1.0" encodin...
[1] 1 <?xml version="1.0" encodin...
[2] 2 <?xml version="1.0" encodin...
#pixeldata property is sparktk frame
>>> pixeldata = dicom.pixeldata.take(1)
>>> pixeldata
[[0L, array([[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 7., 5., ..., 5., 7., 8.],
[ 0., 7., 6., ..., 5., 6., 7.],
...,
[ 0., 6., 7., ..., 5., 5., 6.],
[ 0., 2., 5., ..., 5., 5., 4.],
[ 1., 1., 3., ..., 1., 1., 0.]])]]
def import_dcm(dicom_dir_path, tc=TkContext.implicit):
"""
Creates a dicom object with metadataFrame and pixeldataFrame from a dcm file(s)
Parameters
----------
:param dicom_dir_path: (str) Local/HDFS path of the dcm file(s)
:return: (Dicom) returns a dicom object with metadata and pixeldata frames
Examples
--------
#Path can be local/hdfs to dcm file(s)
>>> dicom_path = "../datasets/dicom_uncompressed"
#use import_dcm available inside dicom module to create a dicom object from given dicom_path
>>> dicom = tc.dicom.import_dcm(dicom_path)
#Type of dicom object created
>>> type(dicom)
#Inspect metadata property to see dicom metadata xml content
>>> dicom.metadata.inspect(truncate=30)
[#] id metadata
=======================================
[0] 0 >> pixeldata = dicom.pixeldata.take(1)
>>> pixeldata
[[0L, array([[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 7., 5., ..., 5., 7., 8.],
[ 0., 7., 6., ..., 5., 6., 7.],
...,
[ 0., 6., 7., ..., 5., 5., 6.],
[ 0., 2., 5., ..., 5., 5., 4.],
[ 1., 1., 3., ..., 1., 1., 0.]])]]
"""
if not isinstance(dicom_dir_path, basestring):
raise ValueError("dicom_dir_path parameter must be a string, but is {0}.".format(type(dicom_dir_path)))
TkContext.validate(tc)
scala_dicom = tc.sc._jvm.org.trustedanalytics.sparktk.dicom.internal.constructors.Import.importDcm(tc.jutils.get_scala_sc(), dicom_dir_path)
from sparktk.dicom.dicom import Dicom
return Dicom._from_scala(tc, scala_dicom)