CoNNECT Support Tools

Several custom support tools have been created to aid in the batch processing. These tools support parallel processing via HTCondor and SGE implemented in the custom batch processing described in the previous section.

Note

FIGURE TO BE INSERTED

bids

Note

the functions of support_tools.bids do not support command line operation.

Python Implementation

support_tools.bids.get_bids_filename(subject: str | None = None, session: str | None = None, acquisition: str | None = None, task: str | None = None, direction: str | None = None, run: str | None = None, process: str | None = None, resolution: str | None = None, space: str | None = None, description: str | None = None, suffix: str | None = None, extension: str | None = None) → str

return bids compliant filename from input labels

get_bids_filename(subject=SUBJECT,session=SESSION,acquisition=ACQUISITION,task=TASK,direction=DIRECTION,run=RUN,process=PROCESS,resolution=RESOLUTION,space=SPACE,description=DESCRIPTION,suffix=SUFFIX,extension=EXTENSION)

Parameters:

  • subject (str, optional) – subject identifier, defaults to None

  • session (str, optional) – session identifier, defaults to None

  • acquisition (str, optional) – acquisition identifier, defaults to None

  • task (str, optional) – task identifier, defaults to None

  • direction (str, optional) – direction identifier, defaults to None

  • run (str, optional) – run identifier, defaults to None

  • process (str, optional) – process identifier, defaults to None

  • resolution (str, optional) – resolution identifier, defaults to None

  • space (str, optional) – space identifier, defaults to None

  • description (str, optional) – description identifier, defaults to None

  • suffix (str, optional) – suffix identifier, defaults to None

  • extension (str, optional) – file externsion, defaults to None

Returns:

BIDS-compliant filename

Return type:

str

support_tools.bids.get_bids_labels(IN_FILE: str) → dict

Get bids compliant filename labels from a file

get_bids_labels(IN_FILE)

Parameters:

IN_FILE (str) – BIDS-compliant filename or filepath

Returns:

bids filename labels

Return type:

dict

condor

Note

the functions of support_tools.condor do not support command line operation.

Python Implementation

support_tools.condor.create_bin_condor_job(jobName: str, exeName: str, machineNames: list, submit: str, error: str, output: str, log: str, dagman: str, docker: bool = False, docker_image: str = 'wsuconnect/neuro', docker_mount_if: str | None = None, request_cpus: int = 1, request_memory: str = '5g')

Creates a pycondor job object to implement a binary from /usr/bin.

create_bin_condor_job(jobName,exeName,machineNames,submit,error,output,log,dagman,docker=False,docker_image=’wsuconenct/neuro’,docker_mount_if=’resshare20’,request_cpus=1,request_memory=’5g’)

Parameters:

  • jobName (str) – name for the parallel htcondor job

  • exeName (str) – helper_function executable name

  • machineNames (list) – list of machine names to to execute jobs on

  • submit (str) – fullpath to condor submit file

  • error (str) – fullpath to condor error file

  • output (str) – fullpath to condor output file

  • log (str) – fullpath to condor log file

  • dagman (pycondor.Dagman) – pointer to created pycondor Dagman object

  • docker (bool, optional) – flag to execute job using a docker container (default False), defaults to False

  • docker_image (str, optional) – docker image for docker execution, defaults to ‘wsuconnect/neuro’

  • docker_mount_if (str, optional) – docker share to mount (see credentials.json), defaults to None

  • request_cpus (int, optional) – number of cpus to allocate to docker container, defaults to 1

  • request_memory (str, optional) – memory in bytes to allocate to docker container, defaults to ‘5g’

Returns:

pointer to a configured pycondor Job object

Return type:

pycondor.Job

support_tools.condor.create_freesurfer_condor_job(jobName: str, exeName: str, machineNames: list, submit: str, error: str, output: str, log: str, dagman: str, docker: bool = False, docker_image: str = 'wsuconnect/neuro', docker_mount_if: str | None = None, request_cpus: int = 1, request_memory: str = '5g')

Creates a pycondor job object to implement FreeSurfer functions.

create_freesurfer_condor_job(jobName,exeName,machineNames,submit,error,output,log,dagman,docker=False,docker_image=’wsuconenct/neuro’,docker_mount_if=’resshare20’,request_cpus=1,request_memory=’5g’)

Parameters:

  • jobName (str) – name for the parallel htcondor job

  • exeName (str) – helper_function executable name

  • machineNames (list) – list of machine names to to execute jobs on

  • submit (str) – fullpath to condor submit file

  • error (str) – fullpath to condor error file

  • output (str) – fullpath to condor output file

  • log (str) – fullpath to condor log file

  • dagman (pycondor.Dagman) – pointer to created pycondor Dagman object

  • docker (bool, optional) – flag to execute job using a docker container (default False), defaults to False

  • docker_image (str, optional) – docker image for docker execution, defaults to ‘wsuconnect/neuro’

  • docker_mount_if (str, optional) – docker share to mount (see credentials.json), defaults to None

  • request_cpus (int, optional) – number of cpus to allocate to docker container, defaults to 1

  • request_memory (str, optional) – memory in bytes to allocate to docker container, defaults to ‘5g’

Returns:

pointer to a configured pycondor Job object

Return type:

pycondor.Job

support_tools.condor.create_fsl_condor_job(jobName: str, exeName: str, machineNames: list, submit: str, error: str, output: str, log: str, dagman: str, docker: bool = False, docker_image: str = 'wsuconnect/neuro', docker_mount_if: str | None = None, request_cpus: int = 1, request_memory: str = '5g')

Creates a pycondor job object to implement FSL functions.

create_fsl_condor_job(jobName,exeName,machineNames,submit,error,output,log,dagman,docker=False,docker_image=’wsuconenct/neuro’,docker_mount_if=’resshare20’,request_cpus=1,request_memory=’5g’)

Parameters:

  • jobName (str) – name for the parallel htcondor job

  • exeName (str) – helper_function executable name

  • machineNames (list) – list of machine names to to execute jobs on

  • submit (str) – fullpath to condor submit file

  • error (str) – fullpath to condor error file

  • output (str) – fullpath to condor output file

  • log (str) – fullpath to condor log file

  • dagman (pycondor.Dagman) – pointer to created pycondor Dagman object

  • docker (bool, optional) – flag to execute job using a docker container (default False), defaults to False

  • docker_image (str, optional) – docker image for docker execution, defaults to ‘wsuconnect/neuro’

  • docker_mount_if (str, optional) – docker share to mount (see credentials.json), defaults to None

  • request_cpus (int, optional) – number of cpus to allocate to docker container, defaults to 1

  • request_memory (str, optional) – memory in bytes to allocate to docker container, defaults to ‘5g’

Returns:

pointer to a configured pycondor Job object

Return type:

pycondor.Job

support_tools.condor.create_python_condor_job(jobName: str, exeName: str, machineNames: list, submit: str, error: str, output: str, log: str, dagman: str, docker: bool = False, docker_image: str = 'wsuconnect/neuro', docker_mount_if: str | None = None, request_cpus: int = 1, request_memory: str = '5g')

Creates a pycondor job object to implement python functions from support_tools.

create_python_condor_job(jobName,exeName,machineNames,submit,error,output,log,dagman,docker=False,docker_image=’wsuconenct/neuro’,docker_mount_if=’resshare20’,request_cpus=1,request_memory=’5g’)

Parameters:

  • jobName (str) – name for the parallel htcondor job

  • exeName (str) – helper_function executable name

  • machineNames (list) – list of machine names to to execute jobs on

  • submit (str) – fullpath to condor submit file

  • error (str) – fullpath to condor error file

  • output (str) – fullpath to condor output file

  • log (str) – fullpath to condor log file

  • dagman (pycondor.Dagman) – pointer to created pycondor Dagman object

  • docker (bool, optional) – flag to execute job using a docker container (default False), defaults to False

  • docker_image (str, optional) – docker image for docker execution, defaults to ‘wsuconnect/neuro’

  • docker_mount_if (str, optional) – docker share to mount (see credentials.json), defaults to None

  • request_cpus (int, optional) – number of cpus to allocate to docker container, defaults to 1

  • request_memory (str, optional) – memory in bytes to allocate to docker container, defaults to ‘5g’

Returns:

pointer to a configured pycondor Job object

Return type:

pycondor.Job

support_tools.condor.create_python_venv_condor_job(jobName: str, exeName: str, machineNames: list, submit: str, error: str, output: str, log: str, dagman: str, docker: bool = False, docker_image: str = 'wsuconnect/neuro', docker_mount_if: str | None = None, request_cpus: int = 1, request_memory: str = '5g')

Creates a pycondor job object to implement python functions from wsuconnect/python3_venv.

create_python_venv_condor_job(jobName,exeName,machineNames,submit,error,output,log,dagman,docker=False,docker_image=’wsuconenct/neuro’,docker_mount_if=’resshare20’,request_cpus=1,request_memory=’5g’)

Parameters:

  • jobName (str) – name for the parallel htcondor job

  • exeName (str) – helper_function executable name

  • machineNames (list) – list of machine names to to execute jobs on

  • submit (str) – fullpath to condor submit file

  • error (str) – fullpath to condor error file

  • output (str) – fullpath to condor output file

  • log (str) – fullpath to condor log file

  • dagman (pycondor.Dagman) – pointer to created pycondor Dagman object

  • docker (bool, optional) – flag to execute job using a docker container (default False), defaults to False

  • docker_image (str, optional) – docker image for docker execution, defaults to ‘wsuconnect/neuro’

  • docker_mount_if (str, optional) – docker share to mount (see credentials.json), defaults to None

  • request_cpus (int, optional) – number of cpus to allocate to docker container, defaults to 1

  • request_memory (str, optional) – memory in bytes to allocate to docker container, defaults to ‘5g’

Returns:

pointer to a configured pycondor Job object

Return type:

pycondor.Job

convert_dicoms.py

convert_dicoms.py

usage: convert_dicoms.py [-h] -i INDIR [--progress]
-h, --help

show this help message and exit

-i <indir>, --in-dir <indir>

(str) fullpath to a sourcedata directory containing DICOM images

--progress

(bool) run in verbose mode

Python Implementation

support_tools.convert_dicoms.convert_dicoms(INDIR: str, PROGRESS: bool = False)

This function converts sourcedata DICOM images to NIfTI images in the input sourcedata directory. This function requires the installation of dcm2niix. Converted NIfTI images are placed in the directory containing the imput sourcedata directory.

convert_dicoms(INDIR,PROGRESS=False)

Parameters:

  • INDIR (str) – fullpath to a sourcedata directory containing DICOM images for conversion

  • PROGRESS (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

copy_dirs.py

Note

the function of support_tools.copy_dirs does not support command line operation.

Python Implementation

support_tools.copy_dirs.copy_dirs(INDIR: str | list, OUTDIR: str, *args, **kwargs)

This function moves or copies input (source) directories to a single output directory.

copy_dirs(OUTDIR,INDIR,move=False)

Parameters:

  • INDIR (str | list) – fullpath to input (source) directory (str) or list of directories

  • OUTDIR (str) – fullpath to an output (destination) directory

  • move (bool, optional) – flag to perform a move instead of a copy, defaults to False

dti_flirt.py

dti_flirt.py

usage: dti_flirt.py [-h] -i IN_FILE -d DATA_DIR -f FLIRT_PARAMS [--flirt-params FLIRT_PARAMS] [--overwrite] [--progress]
-h, --help

show this help message and exit

-i <in_file>

Input DTI file

-d <data_dir>

Project’s directory on disk (see dataDir key in credentials JSON file)

-f <flirt_params>

Path to the FLIRT parameter JSON control file

--flirt-params <flirt_params>
--overwrite
--progress

Python Implementation

support_tools.dti_flirt.dti_flirt(IN_FILE: str, DATA_DIR: str, FLIRT_PARAMS: str, overwrite: bool = False, progress: bool = False)

This function performs FLIRT registration between IN_FILE and structural/standard brain images similar to flirt.py. Registration will be applied to all secondary images in the same directory as IN_FILE.

dti_flirt(IN_FILE,DATA_DIR,FLIRT_PARAMS,overwrite=False,progress=False)

Parameters:

  • IN_FILE (str) – fullpath to a NIfTI file

  • DATA_DIR (str) – fullpath to the project’s data directory (project’s ‘dataDir’ credential)

  • FLIRT_PARAMS (str) – fullpath to project’s 2D ASL FLIRT parameter file

  • overwrite (bool) – OPTIONAL flag to overwrite existing files (default=False)

  • progress (bool) – OPTIONAL flag to display command line output providing additional details on the processing status

Raises:
Returns:

None

dti_preprocess.py

Python Implementation

evaluate_raw_file_transfer.py

Note

the function of support_tools.evaluate_raw_file_transfer does not support command line operation.

Python Implementation

support_tools.evaluate_raw_file_transfer.evaluate_raw_file_transfer(project: str, inDir: str) → bool

This program evaluates files appearing in a single subject/session rawdata directory (inDir). Filenames expected to appear in the rawdata directory are determined from the project’s scan_id.json file found in the project’s code directory.

evaluate_raw_file_transfer(project,inDir)

Parameters:

  • project (str) – target Project’s <project identifier>

  • inDir (str) – fullpath to a single subject/session rawdata directory

Raises:

Exception – general error encountered during execution

Returns:

flag if all expected files exist (True) or don’t (False)

Return type:

bool

feat_full_firstlevel.py

Python Implementation

support_tools.feat_full_firstlevel.feat_full_firstlevel(DATADIR: str, SUBNAME: str, SESNUM: str, FEATDESIGNDIR: str, FEATOUTPUTDIR: str, DESIGNBASENAME: str, reference: str | None = None, step2_design: str | None = None, struc_reg_matrix: str | None = None, progress: bool = False)

This function moves or copies input (source) directories to a single output directory.

feat_full_firstlevel(DATADIR,SUBNAME,SESNUM,FEATDESIGNDIR,FEATOUTPUTDIR,DESIGNBASENAME,reference=None,step2_design=None,struc_reg_matrix=None,progress=False)

Parameters:

  • DATADIR (str) – fullpath to the project’s data directory (<dataDir> key in credentials.json)

  • SUBNAME (str) – subject identifier

  • SESNUM (str) – session identifier

  • FEATDESIGNDIR (str) – directory containing the template feat designs

  • FEATOUTPUTDIR (str) – FEAT output directory

  • DESIGNBASENAME (str) – basename (no extension) for the design file for step 1

  • reference (str, optional) – fullpath to T1 reference image, defaults to None ##DEPRECATED

  • step2_design_basename (str, optional) – basename (no extension) for the design file for step 2, defaults to None

  • struc_reg_matrix (str, optional) – fullpath to the registration matrix between structural (T1) and standard atlas, defaults to None

  • progress (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

Raises:

Exception – general error encountered during execution

flirt_pngappend.py

Note

the function of support_tools.evaluate_raw_file_transfer does not support command line operation.

Python Implementation

support_tools.flirt_pngappend.flirt_pngappend(in_file: str, reference: str, out_file: str)

Creates a registration overlay image (PNG).

Top row contains a background image of in_file in reference space overlaid with the edges of reference Bottom row contains a background image of reference overlaid with the edges of in_file in reference space

flirt_pngappend(in_file,reference,out_file)

Parameters:

  • in_file (str) – fullpath to the input NIfTI image in reference space

  • reference (str) – fullpath to the reference space NIfTI image

  • out_file (str) – fullpath to output png to contain the overlay images

flirt.py

Python Implementation

fsreconall_stage1.py

Python Implementation

exception support_tools.fsreconall_stage1.InvalidJsonInput

Raised when the input JSON control file does not contain the appropriate mandatory definitions

__weakref__

list of weak references to the object (if defined)

support_tools.fsreconall_stage1.fsreconall_stage1(IN_FILE: str, DATA_DIR: str, RECONALL_PARAMS: str, MAINRECONALLOUTPUTDIR: str, directive: str | None = None, overwrite: bool = False, progress: bool = False)

This function performs stage 1 of FreeSurfer reconall freesurfer_recon-all_input.json control file.

fsreconall_stage1(IN_FILE,DATA_DIR,RECONALL_PARAMS,AINRECONALLOUTPUTDIR,directive=None,overwrite=False,progress=False)

Parameters:

  • IN_FILE (str) – fullpath to a NIfTI file

  • DATA_DIR (str) – fullpath to the project’s data directory (project’s ‘dataDir’ credential)

  • RECONALL_PARAMS (str) – fullpath to project’s FreeSurfer RECON-ALL parameter control file

:param MAINRECONALLOUTPUTDIR:fullpath to the desired FreeSurfer SUBJECTS_DIR :type MAINRECONALLOUTPUTDIR: str

Parameters:

  • directive (str, optional) – FreeSurfer workflow directive, defaults to None

  • overwrite (bool, optional) – flag to overwrite existing files, defaults to False

  • progress (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

Raises:

  • InvalidJsonInput – error encountered when the input JSON control file does not contain the appropriate mandatory definitions

  • OSError – OS error encountered during execution

  • Exception – general error encountered during execution

fsreconall_stage2.py

Python Implementation

support_tools.fsreconall_stage2.fsreconall_stage2(STAGE1_DIR: str, DATA_DIR: str, RECONALL_PARAMS: str, overwrite: bool = False, progress: bool = False)

This function performs stage 2 and 3 of FreeSurfer reconall freesurfer_recon-all_input.json control file.

fsreconall_stage2(IN_FILE,DATA_DIR,RECONALL_PARAMS,AINRECONALLOUTPUTDIR,directive=None,overwrite=False,progress=False)

Parameters:

  • STAGE1_DIR (str) – fullpath to a single subject/session reconall Stage 1 directory

  • DATA_DIR (str) – fullpath to the project’s data directory (project’s ‘dataDir’ credential)

  • RECONALL_PARAMS (str) – fullpath to project’s FreeSurfer RECON-ALL parameter control file

  • overwrite (bool, optional) – flag to overwrite existing files, defaults to False

  • progress (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

Raises:

  • InvalidJsonInput – error encountered when the input JSON control file does not contain the appropriate mandatory definitions

  • Exception – general error encountered during execution

get_scan_id.py

Note

the function of support_tools.get_scan_id does not support command line operation.

Python Implementation

support_tools.get_scan_id.get_scan_id(inDir: str, basename: str) → Tuple[str, str, dict]

Get metadata from a source NIfTI file

This program return associated scan information into the custom

get_scan_id(inDir,basename)

Parameters:

  • inDir (str) – fullpath to directory containing NIfTI file

  • basename (str) – basename of input NIfTi file

Raises:

Exception – general error encountered during execution

Returns:

scan name as identified in the Project’s scan_id JSON file within the Project’s ‘code’ directory, bids directory as identified in the Project’s scan_id JSON file within the Project’s ‘code’ directory, scan identifier keys from the scan_id.json control file

Return type:

Tuple[str, str, dict]

mysql.py

Note

the functions of support_tools.mysql do not support command line operation.

Python Implementation

support_tools.mysql.create_mysql_connection(host_name: str, user_name: str, user_password: str, db_name: str, progress, unix_socket: str = '/var/run/mysqld/mysqld.sock') → Connection

This function creates a MySql connection via pymysql.

Parameters:

  • host_name (str) – _description_

  • user_name (str) – _description_

  • user_password (str) – _description_

  • db_name (str)

  • progress (bool) – flag to display command line output providing additional details on the processing status

  • unix_socket (str, optional) – path to pysqld.sock, defaults to ‘/var/run/mysqld/mysqldsock’

Raises:

Exception – general error encountered during execution

Returns:

_description_

Return type:

pymysql.connecttion.Connection

support_tools.mysql.query_file(regex: str, returncol: str = 'fullpath', orderby: str = 'fullpath', inclusion: str | list | None = None, exclusion: str | list | None = None, progress: bool = False) → str

This function queries the table specified in the support_tools.creds.searchTable object for a single file. The fullpath to the single file is returned.

query_file(regexStr,PROGRESS=False)

Parameters:

  • regex (str) – search string for query

  • returncol (str, optional) – table column to return in query, defaults to ‘fullpath’

  • orderby (str, optional) – solumn to sort returns by, defaults to ‘fullpath’

  • inclusion (str | list, optional) – string or list of strings that are additionally required for an item be returned, defaults to None

  • exclusion (str | list, optional) – string or list of strings that will exclude items from being returned, defaults to None

  • progress (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

Returns:

output table column from all items matching the specified search criteria

Return type:

str

support_tools.mysql.query_source_file(regex: str, returncol: str = 'fullpath', orderby: str = 'fullpath', inclusion: str | list | None = None, exclusion: str | list | None = None, progress: bool = False) → str

This function queries the table specified in the support_tools.creds.searchTable object for a single file. The fullpath to the single file is returned.

query_file(regexStr,PROGRESS=False)

Parameters:

  • regex (str) – search string for query

  • returncol (str, optional) – table column to return in query, defaults to ‘fullpath’

  • orderby (str, optional) – solumn to sort returns by, defaults to ‘fullpath’

  • inclusion (str | list, optional) – string or list of strings that are additionally required for an item be returned, defaults to None

  • exclusion (str | list, optional) – string or list of strings that will exclude items from being returned, defaults to None

  • progress (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

Returns:

output table column from all items matching the specified search criteria

Return type:

str

support_tools.mysql.sql_check_table_exists(sqlCursor: Cursor, table: str) → bool

This function checks the database pointed to by the pymysql.cursors.Cursor object for the requested table.

sql_check_table_exists(sqlCursor, table)

Parameters:

  • sqlCursor (pymysql.cursor.Cursors) – open cursor opbject to the database

  • table (str) – target table in the database

Returns:

flag to identify the precense (True) or absence (False) of the specified table in the databaase

Return type:

bool

support_tools.mysql.sql_create_project_tables(progress: bool = False)

This function creates the searchTable and searchSourceTable tables in the database for a given project, all specified in support_tools.creds object.

Parameters:

progress (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

support_tools.mysql.sql_multiple_query(searchtable: str, regex: str, database: str = 'CoNNECT', returncol: str = 'fullpath', searchcol: str = 'filename', orderby: str = 'fullpath', progress: bool = False) → str

Find all items in a MySql table that match the specified search string regex.

Parameters:

  • searchtable (str) – MySql table inside of the specified database

  • regex (str) – string to match in query

  • database (str, optional) – MySql database containing table, defaults to ‘CoNNECT’

  • returncol (str, optional) – table column to return in query, defaults to ‘fullpath’

  • searchcol (str, optional) – table column to perform query, defaults to ‘filename’

  • orderby (str, optional) – solumn to sort returns by, defaults to ‘fullpath’

  • progress (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

Returns:

output table column from all items matching the specified search criteria

Return type:

list

support_tools.mysql.sql_query(searchtable: str, regex: str, database: str = 'CoNNECT', returncol: str = 'fullpath', searchcol: str = 'filename', orderby: str = 'fullpath', inclusion: str | list | None = None, exclusion: str | list | None = None, orinclusion: str | list | None = None, progress: bool = False) → str

Find all items in a MySql table that match the specified search string regex.

Parameters:

  • searchtable (str) – MySql table inside of the specified database

  • regex (str) – string to match in query

  • database (str, optional) – MySql database containing table, defaults to ‘CoNNECT’

  • returncol (str, optional) – table column to return in query, defaults to ‘fullpath’

  • searchcol (str, optional) – table column to perform query, defaults to ‘filename’

  • orderby (str, optional) – solumn to sort returns by, defaults to ‘fullpath’

  • inclusion (str | list, optional) – string or list of strings that are additionally required for an item be returned, defaults to None

  • exclusion (str | list, optional) – string or list of strings that will exclude items from being returned, defaults to None

  • progress (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

Returns:

output table column from all items matching the specified search criteria

Return type:

list

support_tools.mysql.sql_query_dir_check(regex: str, targetdir: str, progress: bool = False) → bool

This function ealuates the presence of files in a specified directory.

Parameters:

  • regex (str) – search string to find matching files

  • targetdir (str) – fullpath to a target directory

  • progress (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

Returns:

presencee (True) or absence (False) of files matching the search string in the specified directory

Return type:

bool

support_tools.mysql.sql_query_dirs(regex: str, source: bool = False, inclusion: str | list | None = None, exclusion: str | list | None = None, progress: bool = False) → list

Find all unique directories containing files in a MySql table that match the specified search string regex.

Parameters:

  • regex (str) – string to match in query

  • source (str, optional) – Utilize searchSourceTable instead of searchTable support_tools.creds object, defaults to False

  • inclusion (str | list, optional) – string or list of strings that are additionally required for an item be returned, defaults to None

  • exclusion (str | list, optional) – string or list of strings that will exclude items from being returned, defaults to None

  • progress (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

Returns:

list of fullpath to unique directories containing files

Return type:

list

support_tools.mysql.sql_table_insert(table: str, item: dict, progress: bool = False)

This function inserts entry(ies) from item into table from the database specified in support_tools.creds object.

sql_table_remove(table,item,progress=True)

Parameters:

  • table (str) – target table in the database

  • item (dict) – dictionary containing the table elements of the item(s) to remove

  • progress (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

support_tools.mysql.sql_table_remove(table: str, item: dict, progress: bool = False)

This function deletes an entry table from the database specified in support_tools.creds object.

sql_table_remove(table,item,progress=True)

Parameters:

  • table (str) – target table in the database

  • item (dict) – dictionary containing the table elements of the item(s) to remove

  • progress (bool, optional) – flag to display command line output providing additional details on the processing status, defaults to False

prepare_examcard_html.py

Note

the function of support_tools.prepare_examcard_html does not support command line operation.

Python Implementation

support_tools.prepare_examcard_html.prepare_examcard_html()

This function .

query_file(INDIR,PROGRESS=False)

Parameters:

  • INDIR (str) – fullpath to a sourcedata directory containing DICOM images for conversion

  • PROGRESS (BOOL) – OPTIONAL flag to display command line output providing additional details on the processing status

Returns:

None

remove_dirs.py

Note

the function of support_tools.remove_dirs does not support command line operation.

Python Implementation

support_tools.remove_dirs.remove_dirs(INDIR: str)

This function moves or copies input (source) directories to a single output directory.

copy_dirs(OUTDIR,INDIR,move=False)

Parameters:

INDIR (str) – fullpath to input (source) directory(ies)

Raises:

Exception – generic error from attenpted deletion

RestToolbox.py

Note

the functions of support_tools.RestToolbox do not support command line operation.

Python Implementation

support_tools.RestToolbox.DoDelete(uri)

Perform an HTTP DELETE on the PACS server

Parameters:

uri (str) – URI to the Orthanc PACS server

Raises:

Exception – generic error connecting to PACS server

Returns:

results of the HTTP PUT or POST request on the PACS server

Return type:

dict

support_tools.RestToolbox.DoGet(uri, data={}, interpretAsJson=True)

Performs an HTTP GET request on the PACS server

Parameters:

  • uri (str) – URI to the Orthanc PACS server

  • data (dict, optional) – supplemental items for the http request, defaults to {}

  • interpretAsJson (bool, optional) – _description_, defaults to True

Raises:

Exception – generic error connecting to PACS server

Returns:

results of the HTTP GET request on the PACS server

Return type:

dict

support_tools.RestToolbox.DoPost(uri, data={}, contentType='')

Performs an HTTP POST request on the PACS server

Parameters:

  • uri (str) – URI to the Orthanc PACS server

  • data (str, dict) – information to post to the PACS server

  • contentType (str) – header content-type if data is str, “” sets contentType to text/plain

Raises:

Exception – generic error connecting to PACS server

Returns:

results of the HTTP PUT or POST request on the PACS server

Return type:

dict

support_tools.RestToolbox.DoPut(uri, data={}, contentType='')

Performs an HTTP PUT request on the PACS server

Parameters:

  • uri (str) – URI to the Orthanc PACS server

  • data (str, dict) – information to post to the PACS server

  • contentType (str) – header content-type if data is str, “” sets contentType to text/plain

Raises:

Exception – generic error connecting to PACS server

Returns:

results of the HTTP PUT or POST request on the PACS server

Return type:

dict