diff --git a/docs/advanced_configuration.md b/docs/advanced_configuration.md deleted file mode 100644 index 2e0353c..0000000 --- a/docs/advanced_configuration.md +++ /dev/null @@ -1,20 +0,0 @@ -# Advanced Configuration - -Can only be configured before building - -## Logging format and levels - -see `app.config.log.py` - -## Timestamp format - -Currently set to `DD.MM.YY HH:MM:SS`. Timestamps are saved to the database as UTC and displayed according to local time - -Change in `app.config.internal_config.py` - -## Background color - -Default: `(204 / 255, 204 / 255, 204 / 255)` - -Change in `app.config.internal_config.py` - diff --git a/docs/build.md b/docs/build.md deleted file mode 100644 index 1847893..0000000 --- a/docs/build.md +++ /dev/null @@ -1,5 +0,0 @@ -# Build Instructions - -A pyinstaller spec file is provided for generating an .exe for Windows. The one-folder option is used for speed. - -Generate and .exe using the command `pyinstaller MainWindow.spec` \ No newline at end of file diff --git a/docs/commandline_usage.md b/docs/commandline_usage.md deleted file mode 100644 index 52774e3..0000000 --- a/docs/commandline_usage.md +++ /dev/null @@ -1,37 +0,0 @@ -# Commandline Interface - -WARNING: The program defaults to the GUI if no arguments are given. - -## Help text - -``` -ImageUntangler Commandline - -optional arguments: - -h, --help show this help message and exit - -f FOLDER, --folder FOLDER - Folder to scan - -s, --scan Generate sequence/metadata report - -o, --org Organize folder data - -t, --time Generate timing report - -v3, --ver3 Load points from v3 -``` - -## Functions - - -### Generate sequence/metadata report -Creates a CSV listing the cases, a list of the sequences available for each case, and the metadata in the heading file for each case - -### Organize folder data -**Not implemented as of v-4.0** - -Re-organizes and anonymizes cases in nested folders into a flat folder sturcture where each case is named 1, 2, 3... - -### Generate timing report: -Creates a CSV listing the cases, the time it took the radiologist to do the "normal" measurement, and the measurement with the centerlines - -### Load points from v3: -Used to migrate from the v3 structure to v4. - -IU v3 used separate JSON files to store the points for each session in a sub-folder inside the case folders called 'data'. This takes those files and merges them into the SQLite database used by v4 diff --git a/docs/configuration.md b/docs/configuration.md deleted file mode 100644 index 35553da..0000000 --- a/docs/configuration.md +++ /dev/null @@ -1,110 +0,0 @@ -# Configuration - -[//]: # (TODO: Finish me) - -A default `config.ini` will be provided if it does not exist at the script directory. - -``` -[folders] -data-folder = C:/ -script-folder = C:/ - -[display] -start-maximized = on -horizontal-number-of-panels = 1 -vertical-number-of-panels = 1 -display-width = 1920 -display-height = 1080 -toolbar-style = icon-and-text -font-size = 30 -window-percentile = 90 -show-interactor-coords = off -text-color = 0, 34, 158 -show-interactor-help = on -help-text-color = 230, 0, 0 -show-interactor-debug = off -debug-text-color = 0, 0, 0 -show-interactor-cursor = on -cursor-color = 255, 0, 0 - -[length-display-style] -color = 55, 230, 128 -highlighted-color = 55, 230, 230 -marker-size = 1 -show-line = on -line-thickness = 10 -line-style = dotted - -[mpr-display-style] -color = 255, 0, 0 -highlighted-color = 253, 184, 255 -marker-size = 1 -line-thickness = 10 -line-style = line - -[mpr-length-display-style] -color = 255, 255, 0 -highlighted-color = 255, 255, 0 -marker-size = 1 -show-line = on -line-thickness = 10 -line-style = line - -[testing] -use-slice-location = on -draw-connecting-lines = on -ignore-uneven-slices = off -point-editing = off -show-memory-usage = on -show-fixer-button = on -show-sliders = off -``` - -## In detail - -### folders -* `data-folder` - Where the MRI data is located. The program needs this to build the complete file paths -* `script-folder` - Location of the script. This is filled automatically during runtime - -### display -* `start-maximized` - self-explanatory. Recommended to start maximized -* `horizontal-number-of-panels` - option to have multiple panels horizontally. **NOT IMPLEMENTED** -* `vertical-number-of-panels` - option to have multiple panels vertically. **NOT IMPLEMENTED** -* `display-width` = Default: 1920 -* `display-height` = Default: 1080 -* `toolbar-style` = Default: icon-and-text **NOT IMPLEMENTED** -* `font-size` = Size of the font in the main display interactor. Default: 30 -* `window-percentile` = Default: 90 -* `show-interactor-coords` = Show the coordinates in the main display interactor as the mouse is moved. **May cause slowdown**. Default: off -* `text-color` = Color of the text in the main display interactor. Default: 0, 34, 158 -* `show-interactor-help` = Shows the help text. Display: on -* `help-text-color` = Color of the help text. Default: 230, 0, 0 -* `show-interactor-debug` = Debugging purposes only. Default: off -* `debug-text-color` = Color of debug text. Default: 0, 0, 0 -* `show-interactor-cursor` = Shows a vertical and horizontal line indicating the location of the mouse. **May cause slowdown**. Default: off -* `cursor-color` = Color of the cursor. Default: 255, 0, 0 - -### length-display-style and mpr-length-display-style - -* color = 55, 230, 128 -* highlighted-color = 55, 230, 230 -* marker-size = 1 -* show-line = on -* line-thickness = 10 -* line-style = dotted - -### mpr-display-style -* color = 255, 255, 0 -* highlighted-color = 255, 255, 0 -* marker-size = 1 -* line-thickness = 10 -* line-style = line - -### testing -* `use-slice-location` - Uses the v3 implementation of the slice location calculation. -* draw-connecting-lines -* ignore-uneven-slices = off -* point-editing = off -* show-memory-usage = on -* show-fixer-button = on -* show-sliders = off diff --git a/docs/index.md b/docs/index.md deleted file mode 100644 index d433e23..0000000 --- a/docs/index.md +++ /dev/null @@ -1,39 +0,0 @@ -# ImageUntangler - -Developed for the Technion Computational MRI lab, this program reads DICOM MRI images and presents a user-friendly interface for radiologists to measure lengths and generate centerlines. - -Developed by Angeleene Ang, Yael Zaffrani, Avraham Kahan, and Moti Freiman. - -## Usage - -GUI: Download the latest release and run the .exe file - -CLI: See [this page](commandline_usage.md) for CLI usage - -## Screenshots - -![](screenshots/open_mri.png) - -![](screenshots/centerline.png) - -## Dependencies - -### For displaying the images -matplotlib -numpy -SimpleITK -vtk - The program was developed using 9.1.0 -pydicom -pynrrd -scipy - -### For the interface -PyQt5 -QtAwesome -pytz - -### Other -pyinstaller -pytest-qt -pytest - diff --git a/docs/maintenance_notes.md b/docs/maintenance_notes.md deleted file mode 100644 index b052c44..0000000 --- a/docs/maintenance_notes.md +++ /dev/null @@ -1,14 +0,0 @@ -# Maintenance Notes - -## Adding functions to toolbar - -* Add button to `gui.display.toolbar.py` with a `clicked.connect(lambda: function(model))` -* Create function in `gui.display.toolbar_connect.py` that refers to the desired functionality in `app.gui_data_handling.case_model.py` -* If the function also needs to interact with the centerline, check if `self.centerline_model` exists in `case_model.py` and add the function in `app.gui_data_handling.centerline_model.py` - -## Creating new file readers - -* Create a new folder under `app.file_reader` -* Create a new reader class, overloading `AbstractReader` -* etc. - diff --git a/docs/metadata.md b/docs/metadata.md deleted file mode 100644 index 3f58e74..0000000 --- a/docs/metadata.md +++ /dev/null @@ -1,2 +0,0 @@ -# Metadata Database - diff --git a/docs/screenshots/centerline.png b/docs/screenshots/centerline.png deleted file mode 100644 index b778892..0000000 Binary files a/docs/screenshots/centerline.png and /dev/null differ diff --git a/docs/screenshots/open_mri.png b/docs/screenshots/open_mri.png deleted file mode 100644 index 9bdad3e..0000000 Binary files a/docs/screenshots/open_mri.png and /dev/null differ diff --git a/docs/test_results/Case flag - Test 1.html b/docs/test_results/Case flag - Test 1.html deleted file mode 100644 index c2c2507..0000000 --- a/docs/test_results/Case flag - Test 1.html +++ /dev/null @@ -1,1540 +0,0 @@ - - - - - Test Results — - - - - - - - - - -
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