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| <div class="section" id="module-apache_beam.io.gcp.dicomio"> |
| <span id="apache-beam-io-gcp-dicomio-module"></span><h1>apache_beam.io.gcp.dicomio module<a class="headerlink" href="#module-apache_beam.io.gcp.dicomio" title="Permalink to this headline">¶</a></h1> |
| <p>DICOM IO connector |
| This module implements several tools to facilitate the interaction between |
| a Google Cloud Healthcare DICOM store and a Beam pipeline.</p> |
| <p>For more details on DICOM store and API: |
| <a class="reference external" href="https://cloud.google.com/healthcare/docs/how-tos/dicom">https://cloud.google.com/healthcare/docs/how-tos/dicom</a></p> |
| <p>The DICOM IO connector can be used to search metadata or write DICOM files |
| to DICOM store.</p> |
| <p>When used together with Google Pubsub message connector, the |
| <cite>FormatToQido</cite> PTransform implemented in this module can be used |
| to convert Pubsub messages to search requests.</p> |
| <p>Since Traceability is crucial for healthcare |
| API users, every input or error message will be recorded in the output of |
| the DICOM IO connector. As a result, every PTransform in this module will |
| return a PCollection of dict that encodes results and detailed error messages.</p> |
| <div class="section" id="search-instance-s-metadata-qido-request"> |
| <h2>Search instance’s metadata (QIDO request)<a class="headerlink" href="#search-instance-s-metadata-qido-request" title="Permalink to this headline">¶</a></h2> |
| <p>DicomSearch() wraps the QIDO request client and supports 3 levels of search. |
| Users should specify the level by setting the ‘search_type’ entry in the input |
| dict. They can also refine the search by adding tags to filter the results using |
| the ‘params’ entry. Here is a sample usage:</p> |
| <blockquote> |
| <div><dl class="docutils"> |
| <dt>with Pipeline() as p:</dt> |
| <dd><dl class="first docutils"> |
| <dt>input_dict = p | beam.Create(</dt> |
| <dd>[{‘project_id’: ‘abc123’, ‘type’: ‘instances’,…}, |
| {‘project_id’: ‘dicom_go’, ‘type’: ‘series’,…}])</dd> |
| </dl> |
| <p>results = input_dict | io.gcp.DicomSearch() |
| results | ‘print successful search’ >> beam.Map( |
| lambda x: print(x[‘result’] if x[‘success’] else None))</p> |
| <p class="last">results | ‘print failed search’ >> beam.Map( |
| lambda x: print(x[‘result’] if not x[‘success’] else None))</p> |
| </dd> |
| </dl> |
| </div></blockquote> |
| <p>In the example above, successful qido search results and error messages for |
| failed requests are printed. When used in real life, user can choose to filter |
| those data and output them to wherever they want.</p> |
| </div> |
| <div class="section" id="convert-dicom-pubsub-message-to-qido-search-request"> |
| <h2>Convert DICOM Pubsub message to Qido search request<a class="headerlink" href="#convert-dicom-pubsub-message-to-qido-search-request" title="Permalink to this headline">¶</a></h2> |
| <p>Healthcare API users might read messages from Pubsub to monitor the store |
| operations (e.g. new file) in a DICOM storage. Pubsub message encode |
| DICOM as a web store path as well as instance ids. If users are interested in |
| getting new instance’s metadata, they can use the <cite>FormatToQido</cite> transform |
| to convert the message into Qido Search dict then use the <cite>DicomSearch</cite> |
| transform. Here is a sample usage:</p> |
| <blockquote> |
| <div>pipeline_options = PipelineOptions() |
| pipeline_options.view_as(StandardOptions).streaming = True |
| p = beam.Pipeline(options=pipeline_options) |
| pubsub = p | beam.io.ReadStringFromPubsub(subscription=’a_dicom_store’) |
| results = pubsub | FormatToQido() |
| success = results | ‘filter message’ >> beam.Filter(lambda x: x[‘success’]) |
| qido_dict = success | ‘get qido request’ >> beam.Map(lambda x: x[‘result’]) |
| metadata = qido_dict | DicomSearch()</div></blockquote> |
| <p>In the example above, the pipeline is listening to a pubsub topic and waiting |
| for messages from DICOM API. When a new DICOM file comes into the storage, the |
| pipeline will receive a pubsub message, convert it to a Qido request dict and |
| feed it to DicomSearch() PTransform. As a result, users can get the metadata for |
| every new DICOM file. Note that not every pubsub message received is from DICOM |
| API, so we to filter the results first.</p> |
| </div> |
| <div class="section" id="store-a-dicom-file-in-a-dicom-storage"> |
| <h2>Store a DICOM file in a DICOM storage<a class="headerlink" href="#store-a-dicom-file-in-a-dicom-storage" title="Permalink to this headline">¶</a></h2> |
| <p>UploadToDicomStore() wraps store request API and users can use it to send a |
| DICOM file to a DICOM store. It supports two types of input: 1.file data in |
| byte[] 2.fileio object. Users should set the ‘input_type’ when initialzing |
| this PTransform. Here are the examples:</p> |
| <blockquote> |
| <div><dl class="docutils"> |
| <dt>with Pipeline() as p:</dt> |
| <dd>input_dict = {‘project_id’: ‘abc123’, ‘type’: ‘instances’,…} |
| path = “gcs://bucketname/something/a.dcm” |
| match = p | fileio.MatchFiles(path) |
| fileio_obj = match | fileio.ReadAll() |
| results = fileio_obj | UploadToDicomStore(input_dict, ‘fileio’)</dd> |
| <dt>with Pipeline() as p:</dt> |
| <dd>input_dict = {‘project_id’: ‘abc123’, ‘type’: ‘instances’,…} |
| f = open(“abc.dcm”, “rb”) |
| dcm_file = f.read() |
| byte_file = p | ‘create byte file’ >> beam.Create([dcm_file]) |
| results = byte_file | UploadToDicomStore(input_dict, ‘bytes’)</dd> |
| </dl> |
| </div></blockquote> |
| <p>The first example uses a PCollection of fileio objects as input. |
| UploadToDicomStore will read DICOM files from the objects and send them |
| to a DICOM storage. |
| The second example uses a PCollection of byte[] as input. UploadToDicomStore |
| will directly send those DICOM files to a DICOM storage. |
| Users can also get the operation results in the output PCollection if they want |
| to handle the failed store requests.</p> |
| <dl class="class"> |
| <dt id="apache_beam.io.gcp.dicomio.DicomSearch"> |
| <em class="property">class </em><code class="descclassname">apache_beam.io.gcp.dicomio.</code><code class="descname">DicomSearch</code><span class="sig-paren">(</span><em>buffer_size=8</em>, <em>max_workers=5</em>, <em>client=None</em>, <em>credential=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/gcp/dicomio.html#DicomSearch"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.gcp.dicomio.DicomSearch" title="Permalink to this definition">¶</a></dt> |
| <dd><p>Bases: <a class="reference internal" href="apache_beam.transforms.ptransform.html#apache_beam.transforms.ptransform.PTransform" title="apache_beam.transforms.ptransform.PTransform"><code class="xref py py-class docutils literal notranslate"><span class="pre">apache_beam.transforms.ptransform.PTransform</span></code></a></p> |
| <p>A PTransform used for retrieving DICOM instance metadata from Google |
| Cloud DICOM store. It takes a PCollection of dicts as input and return |
| a PCollection of dict as results: |
| INPUT: |
| The input dict represents DICOM web path parameters, which has the following |
| string keys and values: |
| { |
| ‘project_id’: str, |
| ‘region’: str, |
| ‘dataset_id’: str, |
| ‘dicom_store_id’: str, |
| ‘search_type’: str, |
| ‘params’: dict(str,str) (Optional), |
| }</p> |
| <dl class="docutils"> |
| <dt>Key-value pairs:</dt> |
| <dd><p class="first">project_id: Id of the project in which the DICOM store is |
| located. (Required) |
| region: Region where the DICOM store resides. (Required) |
| dataset_id: Id of the dataset where DICOM store belongs to. (Required) |
| dicom_store_id: Id of the dicom store. (Required) |
| search_type: Which type of search it is, could only be one of the three |
| values: ‘instances’, ‘series’, or ‘studies’. (Required) |
| params: A dict of str:str pairs used to refine QIDO search. (Optional) |
| Supported tags in three categories: |
| 1.Studies: |
| * StudyInstanceUID, |
| * PatientName, |
| * PatientID, |
| * AccessionNumber, |
| * ReferringPhysicianName, |
| * StudyDate, |
| 2.Series: all study level search terms and |
| * SeriesInstanceUID, |
| * Modality, |
| 3.Instances: all study/series level search terms and |
| * SOPInstanceUID,</p> |
| <p class="last">e.g. {“StudyInstanceUID”:”1”,”SeriesInstanceUID”:”2”}</p> |
| </dd> |
| </dl> |
| <p>OUTPUT: |
| The output dict wraps results as well as error messages: |
| { |
| ‘result’: a list of dicts in JSON style. |
| ‘success’: boolean value telling whether the operation is successful. |
| ‘input’: detail ids and dicomweb path for this retrieval. |
| ‘status’: status code from the server, used as error message. |
| }</p> |
| <p>Initializes DicomSearch. |
| :param buffer_size: # type: Int. Size of the request buffer. |
| :param max_workers: # type: Int. Maximum number of threads a worker can |
| :param create. If it is set to one, all the request will be processed: |
| :param sequentially in a worker.: |
| :param client: # type: object. If it is specified, all the Api calls will |
| :param made by this client instead of the default one: |
| :type made by this client instead of the default one: DicomApiHttpClient |
| :param credential: # type: Google credential object, if it is specified, the |
| :param Http client will use it to create sessions instead of the default.:</p> |
| <dl class="method"> |
| <dt id="apache_beam.io.gcp.dicomio.DicomSearch.expand"> |
| <code class="descname">expand</code><span class="sig-paren">(</span><em>pcoll</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/gcp/dicomio.html#DicomSearch.expand"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.gcp.dicomio.DicomSearch.expand" title="Permalink to this definition">¶</a></dt> |
| <dd></dd></dl> |
| |
| </dd></dl> |
| |
| <dl class="class"> |
| <dt id="apache_beam.io.gcp.dicomio.FormatToQido"> |
| <em class="property">class </em><code class="descclassname">apache_beam.io.gcp.dicomio.</code><code class="descname">FormatToQido</code><span class="sig-paren">(</span><em>credential=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/gcp/dicomio.html#FormatToQido"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.gcp.dicomio.FormatToQido" title="Permalink to this definition">¶</a></dt> |
| <dd><p>Bases: <a class="reference internal" href="apache_beam.transforms.ptransform.html#apache_beam.transforms.ptransform.PTransform" title="apache_beam.transforms.ptransform.PTransform"><code class="xref py py-class docutils literal notranslate"><span class="pre">apache_beam.transforms.ptransform.PTransform</span></code></a></p> |
| <p>A PTransform for converting pubsub messages into search input dict. |
| Takes PCollection of string as input and returns a PCollection of dict as |
| results. Note that some pubsub messages may not be from DICOM API, which |
| will be recorded as failed conversions. |
| INPUT: |
| The input are normally strings from Pubsub topic: |
| “projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/ |
| dicomStores/DICOM_STORE_ID/dicomWeb/studies/STUDY_UID/ |
| series/SERIES_UID/instances/INSTANCE_UID”</p> |
| <p>OUTPUT: |
| The output dict encodes results as well as error messages: |
| { |
| ‘result’: a dict representing instance level qido search request. |
| ‘success’: boolean value telling whether the conversion is successful. |
| ‘input’: input pubsub message string. |
| }</p> |
| <p>Initializes FormatToQido. |
| :param credential: # type: Google credential object, if it is specified, the |
| :param Http client will use it instead of the default one.:</p> |
| <dl class="method"> |
| <dt id="apache_beam.io.gcp.dicomio.FormatToQido.expand"> |
| <code class="descname">expand</code><span class="sig-paren">(</span><em>pcoll</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/gcp/dicomio.html#FormatToQido.expand"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.gcp.dicomio.FormatToQido.expand" title="Permalink to this definition">¶</a></dt> |
| <dd></dd></dl> |
| |
| </dd></dl> |
| |
| <dl class="class"> |
| <dt id="apache_beam.io.gcp.dicomio.UploadToDicomStore"> |
| <em class="property">class </em><code class="descclassname">apache_beam.io.gcp.dicomio.</code><code class="descname">UploadToDicomStore</code><span class="sig-paren">(</span><em>destination_dict</em>, <em>input_type</em>, <em>buffer_size=8</em>, <em>max_workers=5</em>, <em>client=None</em>, <em>credential=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/gcp/dicomio.html#UploadToDicomStore"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.gcp.dicomio.UploadToDicomStore" title="Permalink to this definition">¶</a></dt> |
| <dd><p>Bases: <a class="reference internal" href="apache_beam.transforms.ptransform.html#apache_beam.transforms.ptransform.PTransform" title="apache_beam.transforms.ptransform.PTransform"><code class="xref py py-class docutils literal notranslate"><span class="pre">apache_beam.transforms.ptransform.PTransform</span></code></a></p> |
| <p>A PTransform for storing instances to a DICOM store. |
| Takes PCollection of byte[] as input and return a PCollection of dict as |
| results. The inputs are normally DICOM file in bytes or str filename. |
| INPUT: |
| This PTransform supports two types of input: |
| 1. Byte[]: representing dicom file. |
| 2. Fileio object: stream file object.</p> |
| <p>OUTPUT: |
| The output dict encodes status as well as error messages: |
| { |
| ‘success’: boolean value telling whether the store is successful. |
| ‘input’: undeliverable data. Exactly the same as the input, |
| only set if the operation is failed. |
| ‘status’: status code from the server, used as error messages. |
| }</p> |
| <p>Initializes UploadToDicomStore. |
| :param destination_dict: # type: python dict, encodes DICOM endpoint information: |
| :param {: |
| :param ‘project_id’: str, |
| :param ‘region’: str, |
| :param ‘dataset_id’: str, |
| :param ‘dicom_store_id’: str, |
| :param }: |
| :param Key-value pairs: |
| :param * project_id: Id of the project in which DICOM store locates. (Required) |
| :param * region: Region where the DICOM store resides. (Required) |
| :param * dataset_id: Id of the dataset where DICOM store belongs to. (Required) |
| :param * dicom_store_id: Id of the dicom store. (Required) |
| :param input_type: # type: string, could only be ‘bytes’ or ‘fileio’ |
| :param buffer_size: # type: Int. Size of the request buffer. |
| :param max_workers: # type: Int. Maximum number of threads a worker can |
| :param create. If it is set to one, all the request will be processed: |
| :param sequentially in a worker.: |
| :param client: # type: object. If it is specified, all the Api calls will |
| :param made by this client instead of the default one: |
| :type made by this client instead of the default one: DicomApiHttpClient |
| :param credential: # type: Google credential object, if it is specified, the |
| :param Http client will use it instead of the default one.:</p> |
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