5 releases (3 breaking)
| 0.4.0 | Mar 30, 2021 |
|---|---|
| 0.3.0 | Jan 13, 2021 |
| 0.2.0 | Jan 9, 2021 |
| 0.1.1 | Dec 20, 2020 |
| 0.1.0 | Dec 20, 2020 |
#1716 in Command line utilities
190KB
4.5K
SLoC
orthanc-cli
orthanc-cli is a command-line interface for Orthanc, an open-source, lightweight DICOM server.
Compatibility
orthanc-cli usually supports the same Orthanc versions as its underlying orthanc-rs crate. See Compatibility for details.
Installation
There are multuple different ways to install orthanc-cli.
-
using cargo:
$ cargo install orthanc-cli -
manually downloading a release package from Github Releases page
Completions
orthanc-cli comes with pre-built completion files for Bash, fish and Zsh. See here for details on how to use those files.
Configuration
orthanc-cli needs several settings configured in order to communicate with an Orthanc server: Orthanc server address, and username and password (in case the server requires authentication).
Orthanc server address
Orthanc server address can be set with -s/--server command-line option. The value of the option is an HTTP(S) URL,
e.g. http://127.0.0.1:8042. Alternatively, if you prefer to not type the option every time you call a command, you can
set an environment variable ORC_ORTHANC_SERVER
$ export ORC_ORTHANC_SERVER=http://127.0.0.1:8042
Orthanc server authentication
If the Orthanc server you are working with requires authentication, you can provide it with command-line options
-u/--username and -p/--password. Similar to the server address these can also be set as environment variables
ORC_ORTHANC_USERNAME and ORC_ORTHANC_PASSWORD:
$ export ORC_ORTHANC_USERNAME=orthanc
$ export ORC_ORTHANC_PASSWORD=orthanc
Usage
Help
To get a general idea of the usage run orthanc --help. This will present the list of options, flags, and subcommands:
$ orthanc --help
orthanc-cli 0.4.0
Andrii Yurchuk <ay@mntw.re>
Command-line interface for Orthanc, an open-source, lightweight DICOM server
USAGE:
orthanc [OPTIONS] <SUBCOMMAND>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-s, --server <SERVER> Orthanc server address
-u, --username <USERNAME> Orthanc username
-p, --password <PASSWORD> Orthanc password
SUBCOMMANDS:
patient Patient-level commands
study Study-level commands
series Series-level commands
instance Instance-level commands
modality Modality-level commands
help Prints this message or the help of the given subcommand(s)
Each subommand in its turn has its own has its own help:
$ orthanc study --help
orthanc-study
Study-level commands
USAGE:
orthanc study <SUBCOMMAND>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
SUBCOMMANDS:
list List all studies
show Show study details
search Search for studies
anonymize Anonymize study
modify Modify study
download Download study
delete Delete study
help Prints this message or the help of the given subcommand(s)
Subcommands might have nested subcommands, which also respond to --help. If unsure, append --help to the command to
see how to use it.
Entities and their IDs
orthanc-cli makes a convention of calling Patients, Studies, Series and Instances Entities (not to be confused with Application Entities). You might come across this naming in documentation or names of command-line options or flags.
Similarly to Orthanc web interface orthanc-cli operates mainly with unique identifiers (IDs) when it comes to referring to Entities (Patients, Studies, Series etc.). Each Entity is assigned a unique identifier (ID) by the Orthanc server, that looks similar to this:
22c54cb6-28302a69-3ff454a3-676b98f4-b84cd80a
In the list of Studies for example the identifiers are in the first column (ID):
$ orthanc study list
ID PatientID AccessionNumber StudyInstanceUID StudyDescription StudyDate StudyTime Number of Series
------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ab7a6e26-18072a37-5f2a2210-8a7f0823-f2fa9119 patient_2 REMOVED 1.3.46.670589.11.1.5.0.6560 Study 1 20110101 140606 2
cbec5098-53cd29f5-86d01e4b-c6e76386-709f00a6 patient_1 REMOVED 1.3.46.670589.11.1.5.0.7116 Study 1 20120101 130431 2
8c69229f-eba0eccb-2aa35808-e26bf10a-69375f79 patient_1 REMOVED 1.3.46.670589.11.3540642177 Study 2 20110101 084707 2
When you need to refer to an Entity in any of the orthanc-cli commands use its Orthanc ID:
$ orthanc study show cbec5098-53cd29f5-86d01e4b-c6e76386-709f00a6
ID cbec5098-53cd29f5-86d01e4b-c6e76386-709f00a6
Patient ID 8be8a583-193f48d2-d9b8dd53-adc11459-e46c7c27
PatientID patient_1
StudyID 402411870
AccessionNumber REMOVED
StudyInstanceUID 1.3.46.670589.11.1.5.0.7116.2012100313043060185
StudyDescription Study 1
StudyDate 20120101
StudyTime 130431
Number of Series 2
Search
orthanc-cli allows searching for entities withing the Orthanc server. You can search for patients, studies, series and
instances with orthanc <ENTITY> search --query <QUERY>. Each of the commands will return a list of entities you search
for, e.g. orthanc patient search will return a list of patients, orthanc study search - a list of studies etc.
The value of the --query command-line option are space-separted pairs of DICOM tags: TagName=TagValue. For examle:
$ orthanc series search --query BodyPartExamined=PINKY
ID SeriesInstanceUID SeriesDescription Modality BodyPartExamined Number of Instances
-------------------------------------------------------------------------------------------------------------------------------------------------------
33209de2-5b2e7753-9537bc4d-4bd166f6-fb48d303 1.2.276.0.7230010.3.1.3.816750 Series 1 MR PINKY 1
dab1ca97-70f554a9-c8e83dec-17216f2c-88148c44 1.2.276.0.7230010.3.1.3.816746 Series 1 MR PINKY 1
Wildcards are allowed in values of some DICOM tags. More info on that here.
An example of wildcard usage in StudyDescription:
$ orthanc study search --query AccessionNumber=REMOVED StudyDescription=*1
ID PatientID AccessionNumber StudyInstanceUID StudyDescription StudyDate StudyTime Number of Series
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
342f1834-e4658a76-2f7f8dd6-5f4034dd-eee91323 patient_1 REMOVED 1.2.276.0.7230010.3.1.2.816848 Study 1 20110101 140606 2
92be942a-744ab613-d5ea8167-5b11a0c9-670f0b10 patient_1 REMOVED 1.2.276.0.7230010.3.1.2.816853 Study 1 20110101 140606 2
ab7a6e26-18072a37-5f2a2210-8a7f0823-f2fa9119 patient_2 REMOVED 1.3.46.670589.11.1.5.0.6560.20 Study 1 20110101 140606 4
Anonymizing and modifying Entities
orthanc-cli allows modification and anonymization of entities. Modification requires you to specify how exactly an entity should be modified, while anonymization does not. For both anonymization and modification you can configure the process with either command-line options or a configuration file.
Note that both anonymization and modification create a copy of the entity that is being anonymized/modified instead of changing the entity in-place.
Anonymization
Anonymization of an entity can be done with or without configuration. If done without configuration, anonymization treats DICOM tags according to Application Level Confidentiality Profile Attributes:
$ orthanc study anonymize cbec5098-53cd29f5-86d01e4b-c6e76386-709f00a6
New study ID bb8802bf-fa9621bd-e43406cf-707a3cfb-7786ec34
Patient ID 6cf95a77-4112b9d3-905c17f0-d48ee8e1-b9e6d482
To change the way particular DICOM tags are treated during anonymization you can use command-line options:
--replace: the values of specified DICOM tags will be replaced with those specified--keep: the values of the specified DICOM tags will be left intact (even if they are specified as to be removed in the table mentioned above)--keep-private-tags: whether or not to keep the values of private DICOM tags (if omitted private DICOM tags are removed)
The above command-line options are used as follows:
$ orthanc study anonymize cbec5098-53cd29f5-86d01e4b-c6e76386-709f00a6 --replace PatientName="Rick Sanchez" PatientBirthDate=19700101 --keep StudyDate StudyTime --keep-private-tags
New study ID 72b2983e-0196e005-7102f94f-4bf2161c-18d33b59
Patient ID 1209a543-256b97d2-639bebf1-c3c076e7-0b4b8a3f
If you intend to give special treatment to more than a couple of DICOM tags, writing them all on the command line can become inconvenient. For this purpose you can use an anonymization configuration file instead. The configuration file must be in YAML format and may contain the following fields (see above for their meaning):
replacekeepkeep_private_tags
Example:
replace:
PatientName: Rick Sanchez
PatientBirthDate: 19700101
keep:
- StudyDate
- StudyTime
keep_private_tags: true
The usage of such a configuration file is as follows:
$ orthanc study anonymize cbec5098-53cd29f5-86d01e4b-c6e76386-709f00a6 --config /tmp/anonymization_conf.yml
New study ID 22fc5ba2-650a6ef5-76f78251-af82a47f-87ce33f4
Patient ID 8d8454ca-3c70d505-3d4ddced-792feac4-7c992741
Modification
In order to modify an entity you are required to specify how exactly it should me modified. This can be done with the following command-line options:
--replace: the values of specified DICOM tags will be replaced with those specified--remove: the specified DICOM tags will be removed
The above command-line options are used as follows:
$ orthanc study modify cbec5098-53cd29f5-86d01e4b-c6e76386-709f00a6 --replace PatientName="Rick Sanchez" PatientBirthDate=19700101 --remove StudyDate StudyTime
New study ID 24510c21-3b10e0ac-268f7570-b8c01c22-77e19a41
Patient ID b64615f0-5cac7527-68e751f7-c22d822c-e4ff1e1d
Similar to the process of anonymization you can use a configuration file for modification in case you need to modify more than a hadful of DICOM tags. The configuration file must be in YAML format and may contain the following fields:
replaceremove
Example:
replace:
PatientName: Rick Sanchez
PatientBirthDate: 19700101
remove:
- StudyDate
- StudyTime
The usage of such a configuration file is as follows:
$ orthanc study modify cbec5098-53cd29f5-86d01e4b-c6e76386-709f00a6 --config /tmp/modification_conf.yml
New study ID db0a9bc8-7b0362ca-f361c32b-ba62bfd2-44ff849b
Patient ID 8be8a583-193f48d2-d9b8dd53-adc11459-e46c7c27
Dependencies
~8–13MB
~257K SLoC