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Scans a directory for IMRT QA results

Project description

IMRT-QA-Data-Miner

Scans a directory for IMRT QA results.

Install

pip install iqdm

How to run

To scan a directory for IMRT QA report files and genereate a results .csv file:

iqdm <initial-scan-dir>

To launch a trending dashboard (and open the resulting link):

iqdm <results-csv-file-path>

Screenshot of dashboard:

Command line usage

usage: iqdm [-h] [-ie] [-od OUTPUT_DIR] [-rd RESULTS_DIR] [-all]
            [-of OUTPUT_FILE] [-ver] [-nr] [-df] [-p PORT]
            [-wo WEBSOCKET_ORIGIN]
            [file_path]

Command line interface for IQDM

positional arguments:
  file_path             Initiate scan if directory, launch dashboard if
                        results file

optional arguments:
  -h, --help            show this help message and exit
  -ie, --ignore-extension
                        Script will check all files, not just ones with .pdf
                        extensions
  -od OUTPUT_DIR, --output-dir OUTPUT_DIR
                        Output stored in local directory by default, specify
                        otherwise here
  -rd RESULTS_DIR, --results-dir RESULTS_DIR
                        Results assumed to be stored in local directory by
                        default, specify otherwise here
  -all, --process-all   Process all identified report files, otherwise only
                        new reports will be analyzed
  -of OUTPUT_FILE, --output-file OUTPUT_FILE
                        Output will be saved as <report_type>_results_<time-
                        stamp>.csv by default. Define this tag to customize
                        file name after <report_type>_
  -ver, --version       Print the IQDM version
  -nr, --no-recursive-search
                        Include this flag to skip sub-directories
  -df, --day-first      Assume day first for ambiguous dates in trending
                        dashboard
  -p PORT, --port PORT  Specify port of trending dashboard webserver
  -wo WEBSOCKET_ORIGIN, --allow-websocket-origin WEBSOCKET_ORIGIN
                        Allow a websocket origin other than localhost, see
                        bokeh documentation

Notes

This script was written specifically for SNC Patient and Delta4, but I'd be happy to include support for other vendors if someone could provide some anonymized example reports.

Vendor Compatibility

  • Sun Nuclear: SNC Patient
  • ScandiDos: Delta4
    This is still in beta, but the reported csv data is largely correct (reported energy might be off). The class parses much more data (including individual beam results), but isn't currently in csv nor validated.

Contributing

If you'd like to contribute code to support a new vendor, please create a new python file in the parsers directory containing a new class. This class should include the following to be compatible:

  • PROPERTIES

    • identifiers
      this is a list of strings that collectively and uniquely are found in a report type
    • columns
      a list of strings indicating the columns of the csv to be output
    • csv
      a string of values for each column, delimited with DELIMITER in utilities.py
    • report_type
      a string succinctly describing the report, this will be used in the results filename created in main.py
  • METHODS

    • process_data(text_data)
      processing the data does not occur until this is called

Project details


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Files for IQDM, version 0.3.1.post1
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