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Help for programmers

Starting virt env from scratch

  • conda create --name viQC
  • conda activate viQC
  • cd C:....\imageQCpy
  • pip install -e .

For using pytest:

  • pip install pytest
  • pip install pytest-qt

using virt env later

  • conda activate viQC
  • cd C:...\imageQCpy
  • python -m imageQC.imageQC # to run the program
  • python -m pytest tests\test_calculations.py # example to test

To be able to use breakpoints:

  • Find developer_mode in imageQC.py (currently at line 198) and set this variable from False to True.

To be able to plot during pytest or breakpoints:

  • import matplotlib.pyplot as plt
  • plt.plot([x,y]) or plt.imshow(some_array)
  • plt.pause(.1)

Help to find any text in code

To easily find out where a method or class is used or if any breakpoints are left, one could use imageQCpy/helper_scripts/search_files.py. Edit the content of variable search_string and run the script. This will list all files and line numbers where the search_string is found within directory src.

Update resources.py after changes

If adding icons or file-based default configuration settings, resources.qrc will have to be updated and a new resources.py need de be recreated. If adding icons, a dark-mode icon is also needed.

  • add file to folder icons or config_defaults and add file name to resouces.qrc
  • cd C:...\imageQCpy\src\imageQC
  • pyrcc5 resources.qrc -o resources.py

Adding new modality

  • add modality to all relevant dictionaries in config/iQCconstants.py
  • add ParamSet in config/config_classes.py + add this to class ParamSet and add paramsets_ in LastModified
  • add ParamsTab in ui/ui_main_test_tabs.py
  • add default DCM settings in config_defaults/tag_patterns_test_dcm.yaml (and re-run pyrcc5 as explained above)
  • add Modality to dash_app (table_overview)
  • consider adding variants to scripts/dcm.py - get_modality

When adding new parameters and variants to a test

  • if alternative to current test: add result table headers in config/iQCconstants.py HEADERS (and HEADERS_SUP if supplement data) (and optionally ALTERNATIVES)
  • add configurable parameters in config/config_classes.py ParamSet<Modality> (or ParamsetCommon if available to all paramsets), starting with the testcode (three letters)
  • else follow instructions for adding testcode (below)

When adding new testcode (analyse type)

  • add testcode (three letters at least first capital) in config/iQCconstants.py QUICKTEST_OPTIONS same order as tabs for the tests
  • add result table headers in config/iQCconstants.py HEADERS (and HEADERS_SUP if supplement data) (and ALTERNATIVES if alternative headers)
  • add configurable parameters in config/config_classes.py ParamSet<Modality> (or ParamsetCommon if available to all paramsets)
  • add GUI in ui/ui_main_test_tabs.py TestTab<Modality> order of tabs should fit QUICKTEST_OPTIONS order
    • self.<same as paramname in ParamSet> as gui element
    • if same as for other modality consider adding (moving) create_tab_<testcode> to the Common tab
    • verify that type of widget supported by params_changed_from_gui and update_displayed_params
  • add roi in scripts/calculate_roi.py (in get_rois method <testcode>)
  • if more than four colored rois / other visualization needs: add visualization of roi in ui/ui_image_canvas - ImageCanvas.roi_draw()
  • add test calculations to calculate_qc
  • add test visualizations to plot canvas (ui/ui_main_result_tabs - ResultPlotCanvas)
    • and optionally result image canvas (ui/ui_image_canvas - ResultImageCanvas)
  • if more ALTERNATIVES or dynamic HEADERS given in iQCconstants - note the comments above these parameters within iQCconstants.py

When adding new types of templates (settings)

  • add to iQCconstants CONFIG_FNAMES
  • add template type to config_classes + add to last_modified
  • start with a widget (inheriting from StackWidget of settings_reusables) that will have a similar use
  • create the widgets and add to SettingsDialog init (settings.py)
  • in config_func.py load_settings - add code to if fname == '<the new fname>'
  • if more than only the fname to load:
    • search for "'patterns'" in settings_reusables.py - you will probably have to make these places work for you new template
  • if coupled in auto_template or paramset or tag_infos by labels/attribute names - consider warnings (verify_auto_template /
  • consider add to
    • MainWindow (update settings) if affect processes in main window
    • ImportMain (settings.py) if settings should be available for import (if yaml file it should be)
    • syncronize StackWidget update_from_yaml with SettingsDialog import from yaml + update_import main
    • InputMain (input_main_auto.py) if affect processes in calculate_qc or run_automation_non_gui/open_automation, run_template
  • if not modality_dict:
    • add code to SettingsDialog - update_import_main, get_marked
    • SharedSettings - verify_config_files
  • if PositionTable to set column headers - settings_reusables.py QuickTestOutputSubDialog elif testcode == in update data

Update requirements.txt

  • cd to src-folder
  • pipreqs
  • requirements will now be in the src-folder. Move it to folder above src.
  • remove skimage...?
  • remove charset_normalizer (only for pyinstaller)
  • remove plotly/dash_core_components/dash_html_components (already included with dash)
  • Copy also new content to setup.cfg

Update pdf version of Wiki

Note that code used by wikidoc are within the .md files of imageQCpy/wiki

For building .exe

This method reduces from ~300 MB vs ~1,2 GB compared to doing this in conda environment:

  • Install python 3.9.7 and choose to add path
  • Create an empty folder (somewhere) called imageQCpy. This folder should hold the input and output for pyinstaller.
  • Copy into the empty folder src and all files directly from folder above src except .gitignore/.pylintrc
  • Delete these folders in src: icons, config_defaults + all pycache/eggs folders
  • Delete also resources.qrc
  • In cmd.exe (not from Anaconda):
    • cd ....path...to...\imageQCpy (the new stripped folder)
  • pip install -e .
    • (if error on cwd None, try this: pip install --upgrade pip setuptools wheel --user)
  • pip install pyinstaller (or pip list to see if its already installed)
  • maybe: pip uninstall pathlib (have had some troubles and this solved it)

pyinstaller -i="iQC_icon.ico" --clean --hidden-import=['charset_normalizer.md__mypyc'] --collect-submodules=pydicom --paths=src\imageQC src\imageQC\imageQC.py

  • avoid -w (--windowed) to make argparse work running imageQC with arguments for automation. Drawback is that cmd window always shown.

Fixed missing module when using import-hidden by adding from charset_normalizer import md_mypyc

  • Create an empty config_defaults folder in folder dist (result from pyinstaller process)

  • Copy NM_Auto_QC from the original config_defaults to this new empty folder.

  • Add latest pdf user manual to dist.

  • zip content of folder dist to distribute imageQCpy_versionXXX.zip

To run the exe file from cmd.exe:

  • cd .....\dist\imageQC
  • imageQC <arg1> <arg2>