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2. px find
Rudolph Pienaar edited this page Sep 26, 2019
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px-find is a wrapper around dcmtk findscu.
px-find finds series on a PACS server given a vast array of parameters. See px-find --help for the full list. In stand-alone cases, px-find will often be used to Query a PACS. The results can be presented in a console friendly formatted report.
px-find sends query keys to an SCP and awaits responses.
The application can be used to test SCPs of the Query/Retrieve
and Basic Worklist Management Service Classes.
-- DCMTK, about findscu.
px-find --desc _script mode_:
px-find \
[--aet <AETitle>] \
[--aec <CalledAETitle>] \
[--serverIP <PACSserverIP>] \
[--serverPort <PACSserverPort>] \
[--findscu <findscuAbsolutePath>] \
[--movescu <movescuAbsolutePath>] \
[--PatientID <MRN>] \
[--PatientName <ExactPatientName>] \
[--PatientSex <M_or_F>] \
[--StudyDate <YYYY/MM/DD>] \
[--ModalitiesInStudy <Modalities>] \
[--Modality <ModalityToQuery>] \
[--PerformedStationAETitle <StationTitle>] \
[--StudyDescription <studyDescription>] \
[--SeriesDescription <seriesDescription>] \
[--StudyInstanceUID <studyInstanceUID>] \
[--SeriesInstanceUID <seriesInstanceUID>] \
[--retrieve [--move]] \
[--reportTags <JSONDesc>] \
[--colorize light|dark] \
[--printReport tabular|rawText|json] \
[--waitForUserTerminate] \
[-x|--desc] \
[-y|--synopsis] \
[--version] \
[--debugToDir <dir>] \
[--verbosity <level>] [--aet <AETitle>]
The AETitle of *this* entity.
[--aec <CalledAETitle>]
The called AETitle of *this* entity. Needed for some PACS systems.
[--serverIP <PACSserverIP>]
The IP of the PACS server.
[--serverPort <PACSserverPort>]
The port associated with the PACS server.
[--executable <findscuAbsolutePath>]
The absolute location of the 'findscu' executable.
[--PatientID <MRN>]
The patient ID on which to Query.
[--PatientName <ExactPatientName>]
The patient name on which to Query.
[--PatientSex <M_or_F>]
The patient sex (largely irrelevant since open ended searches are
not supported by most PACS servers).
[--StudyDate <YYYY/MM/DD>]
Filter results by <studyDate>.
[--ModalitiesInStudy <Modalities>]
Filter by modalities in study.
[--Modality <Modality>]
The modality to filter.
[--PerformedStationAETitle <StationTitle>]
Filter by station ID.
[--StudyDescription <studyDescription>]
Filter by study description.
[--SeriesDescription <seriesDescription>]
Filter by series description.
[--StudyInstanceUID <studyInstanceUID>]
Filter by study instance UID.
[--SeriesInstanceUID <seriesInstanceUID>]
Filter by series instance UID.
[--retrieve]
If set, perform a DICOM movescu on the set of filtered
SeriesInstanceUIDs using internal calls.
[--move]
If set and called with [--retrieve], perform a DICOM movescu on the
set of filtered SeriesInstanceUIDs using the pypx/move module.
[--reportTags <JSONdesc>]
If specified, print only the JSON specified result tags from either the
STUDY or SERIES level.
[--colorize 'light'|'dark']
An optional directive to colorize the report output, either for 'light'
or 'dark' consoles.
[--printReport tabular|rawText|json]
If specified, pretty print a report in a variety of formats.
[--waitForUserTerminate]
If specified, wait at program conclusion for explicit user termination.
This is useful in dockerized runs since PACS data might still be
in flight when the program ends, and terminating the program then
will result in non reception of outstanding data.
[-x|--desc]
Provide an overview help page.
[-y|--synopsis]
Provide a synopsis help summary.
[--version]
Print internal version number and exit.
[--debugToDir <dir>]
A directory to contain various debugging output -- these are typically
JSON object strings capturing internal state. If empty string (default)
then no debugging outputs are captured/generated. If specified, then
``pfcon`` will check for dir existence and attempt to create if
needed.
[-v|--verbosity <level>]
Set the verbosity level. "0" typically means no/minimal output. Allows for
more fine tuned output control as opposed to '--quiet' that effectively
silences everything. px-find \
--aec CHRIS \
--aet FNNDSC-CHRISDEV \
--serverIP 134.174.12.21 \
--serverPort 104 \
--PatientID 4777764 \
--colorize dark \
--reportTags \
'{
"header":
{
"study" : [
"PatientName",
"ScanDate",
"AccessionNumber",
"PatientID",
"PatientSex",
"PatientAge",
"PerformedStationAETitle",
"StudyDescription"
]
},
"body":
{
"series" : [
"SeriesDescription"
]
}
}'
px-find \
--aec CHIPS \
--aec ORTHANC \
--serverIP localhost \
--serverPort 4242 \
--PatientID LILLA-9731 \
--colorize dark \
--reportTags \
'{
"header":
{
"study" : [
"PatientName",
"ScanDate",
"AccessionNumber",
"PatientID",
"PatientSex",
"PatientAge",
"PerformedStationAETitle",
"StudyDescription"
]
},
"body":
{
"series" : [
"SeriesDescription"
]
}
}' docker run --rm -ti \
-p 10402:10402 \
-v /tmp:/dicom \
fnndsc/pypx \
--px-find \
--aet CHIPS \
--aec ORTHANC \
--serverIP 10.72.76.155 \
--serverPort 4242 \
--PatientID LILLA-9731 \
--colorize dark \
--reportTags \
'{
"header":
{
"study" : [
"PatientName",
"ScanDate",
"AccessionNumber",
"PatientID",
"PatientSex",
"PatientAge",
"PerformedStationAETitle",
"StudyDescription"
]
},
"body":
{
"series" : [
"SeriesDescription"
]
}
}'
docker run --rm -ti \
-p 10402:10402 \
-v /tmp:/dicom \
fnndsc/pypx \
--px-find \
--aec CHRIS \
--aet FNNDSC-CHRISDEV \
--serverIP 134.174.12.21 \
--serverPort 104 \
--PatientID 4777764 \
--colorize dark \
--reportTags \
'{
"header":
{
"study" : [
"PatientName",
"StudyDate",
"AccessionNumber",
"PatientID",
"PatientSex",
"PatientAge",
"PerformedStationAETitle",
"StudyDescription"
]
},
"body":
{
"series" : [
"SeriesDescription"
]
}
}'
## Python module syntax
px-find module
-------------------
```python
# in yourscript.py
import pypx
pacs_settings = {
'executable': '/usr/bin/findscu',
'aec': 'ORTHANC',
'aet': 'CHIPS',
'serverIP': '127.0.0.1',
'serverPort': '4242',
}
# query parameters
query_settings = {
'PatientID': 'LILLA-9731'
}
# output parameters
output_settings = {
'printReport': 'json',
'colorize': 'dark'
}
# python 3.5 ** syntax
output = pypx.find({
**pacs_settings,
**query_settings,
**output_settings})Will return in the output['report']['json']
[
{
"header": {
"PatientName": "LILLA-9731",
"PatientBirthDate": "19000101",
"StudyDate": "20111206",
"PatientAge": "017M",
"PatientSex": "M",
"AccessionNumber": "22268454",
"PatientID": "LILLA-9731",
"PerformedStationAETitle": "no value provided",
"StudyDescription": "anonymized",
"Modality": "MR"
},
"body": [
{ "SeriesDescription": "T2 SPC SAG OBL LT IAC" },
{ "SeriesDescription": "T2 SPC AXIAL THRU IAC'S" },
{ "SeriesDescription": "T2 SPC SAG OBL RT IAC" },
{ "SeriesDescription": "AAHScout" },
{ "SeriesDescription": "AX MPRAGE RECON" },
{ "SeriesDescription": "mocoMEMPRAGE_192FOV RMS" },
{ "SeriesDescription": "COR MPRAGE RECON" },
{ "SeriesDescription": "ep_moco_nav_set (move FOV above shoulders)" },
{ "SeriesDescription": "AX T2 FLAIR" },
{ "SeriesDescription": "AAHScout_MPR" },
{ "SeriesDescription": "AX FSE T2" }
],
"bodySeriesUID": [
{ "SeriesInstanceUID": "1.3.12.2.1107.5.2.32.35235.2011120608261498976230921.0.0.0" },
{ "SeriesInstanceUID": "1.3.12.2.1107.5.2.32.35235.2011120608154426308230611.0.0.0" },
{ "SeriesInstanceUID": "1.3.12.2.1107.5.2.32.35235.2011120608335936039431226.0.0.0" },
{ "SeriesInstanceUID": "1.3.12.2.1107.5.2.32.35235.2011120607520430264805764.0.0.0" },
{ "SeriesInstanceUID": "1.3.12.2.1107.5.2.32.35235.30000011120415032007800030559" },
{ "SeriesInstanceUID": "1.3.12.2.1107.5.2.32.35235.2011120607550716203206654.0.0.0" },
{ "SeriesInstanceUID": "1.3.12.2.1107.5.2.32.35235.30000011120415032007800029729" },
{ "SeriesInstanceUID": "1.3.12.2.1107.5.2.32.35235.2011120607550721381806658.0.0.0" },
{ "SeriesInstanceUID": "1.3.12.2.1107.5.2.32.35235.2011120608060183769230384.0.0.0" },
{ "SeriesInstanceUID": "1.3.12.2.1107.5.2.32.35235.2011120607520430331505768.0.0.0" },
{ "SeriesInstanceUID": "1.3.12.2.1107.5.2.32.35235.2011120608041225195630230.0.0.0" }
]
}
]
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