us2mathias/echoloader repository overview

usage: us2mathias/echoloader 
                  [-h] [--src SRC] [--src-details SRC_DETAILS] [--dst DST [DST ...]] [--watch] [--watch-sub-dirs] [--pacs] [--secure SECURE SECURE SECURE] [--pacs-ae-title PACS_AE_TITLE]
                  [--pacs-port PACS_PORT] [--delete_original] [--n N] [--upload] [--upload-retries UPLOAD_RETRIES] [--upload-retry-interval UPLOAD_RETRY_INTERVAL] [--env ENV] [--extracted EXTRACTED]       
                  [--extracted-details EXTRACTED_DETAILS [EXTRACTED_DETAILS ...]] [--csv-out CSV_OUT] [--verbose] [--save-failed SAVE_FAILED] [--no-anonymization]
                  [--pseudonymize PSEUDONYMIZE [PSEUDONYMIZE ...]] [--pseudonymize-file PSEUDONYMIZE_FILE] [--no-compression] [--customer CUSTOMER] [--customer-aet] [--sync-mode SYNC_MODE]
                  [--sync SYNC [SYNC ...]] [--sync-url] [--sync-main-findings] [--sync-pdf-images] [--sync-designators SYNC_DESIGNATORS [SYNC_DESIGNATORS ...]]
                  [--sync-modalities SYNC_MODALITIES [SYNC_MODALITIES ...]] [--sync-poll SYNC_POLL] [--sync-stale SYNC_STALE] [--sync-from SYNC_FROM] [--sync-by-measurement]
                  [--sync-search SYNC_SEARCH [SYNC_SEARCH ...]] [--sync-mapping SYNC_MAPPING] [--sync-regulatory-status] [--sync-edited-status] [--sync-annotations] [--sync-comments]
                  [--sync-generate-uid] [--sync-same-series] [--sync-pdf-as-sc] [--sync-ds-always-render] [--sync-ds-standardize] [--overwrite-tags [OVERWRITE_TAGS ...]] [-v V] [-y] [--username USERNAME]  
                  [--password PASSWORD] [--pacs-tls] [--enforce-ae-title] [--config-file CONFIG_FILE] [--app-config] [--trial TRIAL] [--proxy PROXY] [--log LOG] [--filter FILTER [FILTER ...]]
                  [--src-glob SRC_GLOB] [--params-trial PARAMS_TRIAL [PARAMS_TRIAL ...]] [--params-pid PARAMS_PID [PARAMS_PID ...]] [--params-visit PARAMS_VISIT [PARAMS_VISIT ...]] [--trial-id TRIAL_ID]   
                  [--use-echoloader-settings] [--control-center]

options:
  -h, --help            show this help message and exit
  --src SRC             Source folder
  --src-details SRC_DETAILS
                        Regular expression to apply on path to extract patient details used in the upload request. Can use (?P<key>re) to capture regular expression re to key. Key can be trial,
                        patient_id, visit_id or filename
  --dst DST [DST ...]   Destination folder or DICOM destination
  --watch               Watch the src folder for changes
  --watch-sub-dirs      Watch only sub directories for changes
  --pacs                Starts PACS server
  --secure SECURE SECURE SECURE
                        Enable Secure PACS, must include 3 arguments which are paths to: CA certificate, server certificate and server key
  --pacs-ae-title PACS_AE_TITLE
                        PACS AE Title, defaults to Us2.ai
  --pacs-port PACS_PORT
                        PACS port, defaults to 11112
  --delete_original     Delete original files after processing
  --n N                 Number of workers
  --upload              Upload processed images to Us2.ai
  --upload-retries UPLOAD_RETRIES
                        Number of retries for upload
  --upload-retry-interval UPLOAD_RETRY_INTERVAL
                        Interval between retries for upload
  --env ENV             The Us2.ai environment to use
  --extracted EXTRACTED
                        File of cases to ignore - csv file with customer, trial, patientID, visit, filename
  --extracted-details EXTRACTED_DETAILS [EXTRACTED_DETAILS ...]
                        Details to use for matching extraction
  --csv-out CSV_OUT     Path to csv file of extracted cases
  --verbose             Enable all application debug/info logs
  --save-failed SAVE_FAILED
                        Path to store failed cases locally
  --no-anonymization    No anonymization of data prior to upload
  --pseudonymize PSEUDONYMIZE [PSEUDONYMIZE ...]
                        DCM tags to pseudonymize
  --pseudonymize-file PSEUDONYMIZE_FILE
                        Path to file for pseudonymization mapping
  --no-compression      Don't compress videos into mp4 format
  --customer CUSTOMER   The customer tag used for the upload
  --customer-aet        Whether or not customer should be derived from AET
  --sync-mode SYNC_MODE
                        The sync mode to use, can be 'SIMPLE' or 'ADVANCED'
  --sync SYNC [SYNC ...]
                        Will try to sync structured report back to specified location.Format: IP:PORT:REMOTE_AE_TITLE[:LOCAL_AE_TITLE:CERT:KEY][&MODALITIES]
  --sync-url            Include url to measurement page in SR export
  --sync-main-findings  Include main findings in SR export/DICOM encapsulated PDF
  --sync-pdf-images     Include images in DICOM encapsulated PDF
  --sync-designators SYNC_DESIGNATORS [SYNC_DESIGNATORS ...]
                        Designators used for SR export
  --sync-modalities SYNC_MODALITIES [SYNC_MODALITIES ...]
                        Modalities that should be synced to PACS, valid values are SR, PS, SC
  --sync-poll SYNC_POLL
                        Delay between polls
  --sync-stale SYNC_STALE
                        Number of seconds that exam needs to be stale before it is synced
  --sync-from SYNC_FROM
                        The time point from which to sync, expression must return datetime
  --sync-by-measurement
                        Will cause all PS/SC files to contain just one measurement each, instead of all for the frame
  --sync-search SYNC_SEARCH [SYNC_SEARCH ...]
                        Parameters for sync search, can be used to sync only when special criteria is met
  --sync-mapping SYNC_MAPPING
                        Tag for custom mapping to use
  --sync-regulatory-status
                        Will attach regulatory status in SR document
  --sync-edited-status  Will attach measurement edit status in SR document
  --sync-annotations    Will include measurement annotations and image references in SR document
  --sync-comments       Will include comments in SR document
  --sync-generate-uid   Generate a random SOPInstanceUID instead of using the deterministic UID from the backend
  --sync-same-series    Use the same SeriesInstanceUID for the same study
  --sync-pdf-as-sc      Send PDF report pages as Secondary Captures
  --sync-ds-always-render
                        Output original DICOM if available
  --sync-ds-standardize
                        Standardize output to match study details in Us2.ai
  --overwrite-tags [OVERWRITE_TAGS ...]
                        Tags to override for specific output modalities, in the format MODALITY:TAG=VALUE
  -v V                  Version of API to use
  -y                    Answer yes to all prompts
  --username USERNAME   App username
  --password PASSWORD   App password
  --pacs-tls            Start PACS(TLS) server
  --enforce-ae-title    Enforces that users have configured a proper AE title in the UI
  --config-file CONFIG_FILE
                        Configuration file for the EchoLoader
  --app-config          Read config from application(cloud/on-prem) instead of config file
  --trial TRIAL         Trial name of studies to upload
  --proxy PROXY         Spin up a proxy against env on the given port
  --log LOG             File for logs
  --filter FILTER [FILTER ...]
                        Inclusive filter for DS files to process
  --src-glob SRC_GLOB   glob expression to apply on src directory
  --params-trial PARAMS_TRIAL [PARAMS_TRIAL ...]
                        The dicom fields to check for trial
  --params-pid PARAMS_PID [PARAMS_PID ...]
                        The dicom fields to check for patient ID
  --params-visit PARAMS_VISIT [PARAMS_VISIT ...]
                        The dicom fields to check for visit ID
  --trial-id TRIAL_ID   ID of the trial where all data should be uploaded
  --use-echoloader-settings
                        Use the web application echoloader settings for anonymization
  --control-center      Connect to Us2.ai control center