LungCTAnalyzer in macOS: missing os.startfile

Support
1

@rbumm

In LungCTAnalyzer 2.49 in Slicer 5.0.2 in macOS 12.4 with Python 3.9.10, when generating PDF report: report is generated in LungCTAnalyzerReports but Python Interactor shows

modules/LungCTAnalyzer.py", line 843, in onCreatePDFReportButton
    os.startfile(reportPath.replace('/', '\\'))
AttributeError: module 'os' has no attribute 'startfile'

Seems os.startfile is Windows-specific, and macOS may need os.system("open myFile").

The error is not seen with Create CSV file (after PDF report generation).

2

Yes, that call is windows specific. It would be great if someone could contribute a fix to generalize the code.

https://docs.python.org/3/library/os.html#os.startfile

3

Thank you @pieper .

I think this fixed the problem.

@ashipde could you

image

in the extension manager tomorrow or the day after that, then update the Lung CT Analyzer and test again? I have no MAC or Linux available …

Thank you.

4

@rbumm Thank you for the quick-fix. The error does not appear, but on macOS, the generated PDF report is not opened automatically, which I believe is the intent. In error messages I see: The file /\Users\ashipde\Documents\LungCTAnalyzerReports\[redacted].pdf does not exist. But the file exists… seems backslashes are the issue (macOS/Unix using forward ones unlike Windows).

1 Like
5

Thank you. I removed the backslash generation in the PDF path for macOS and Linux.
Could you test again?

6

The file-missing error is gone after the latest fix. Interactor window shows Starting '/Users/ashipde/Documents/LungCTAnalyzerReports/[redacted].pdf' .... However, the PDF file does not auto-open. My system Python opens the file in PDF viewer app with subprocess.call(['open', '/Users/ashipde/Documents/LungCTAnalyzerReports/[redacted].pdf']), so not sure what may be the issue.

7

@ashipde please try if the same subprocess call opens the file in Slicer’s Python interactor. If it does not work then you may need to use the startup environment.

8

My mistake. The report file does auto-open as expected with the latest GitHub download of the extension. May be my extension uninstall/re-install was not done properly by me.

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