updated to allow for radiobuttons and numerous bug fixes

README.md

@@ -14,6 +14,21 @@ Primarily for use on Mac OS X, but should work on Linux and Windows.
 
 > **Warning:** Please note that this application is still in development and there may be unresolved bugs and issues. Use at your own risk!
 
+## Table of Contents
+- [Installation](#installation)
+- [Usage](#usage)
+  - [Inputs and Outputs](#inputs-and-outputs)
+    - [Checkboxes](#checkboxes)
+    - [Bounding Boxes](#bounding-boxes)
+    - [Radiobuttons](#radiobuttons)
+  - [Progress](#progress)
+  - [Keyboard Shortcuts](#keyboard-shortcuts)
+- [Customisation](#customisation)
+  - [Configuration Wizard](#configuration-wizard)
+  - [YAML File](#yaml-file)
+- [Backup Files](#backup-files)
+- [Executable Application](#executable-application)
+
 Installation
 ------------
 
@@ -45,9 +60,9 @@ speedy_qc
 
 Alternatively, the app may be run from an executable (see below).
 
-### Outputs
+### Inputs and Outputs
 
-Outputs are stored in a .json file in a directory chosen by the user.
+#### Checkboxes
 
 Checkboxes are stored as integers:  
 
@@ -57,20 +72,25 @@ Checkboxes are stored as integers:
 |        1        |  Uncertain  |
 |        2        | True / Yes  |
 
-### Bounding Boxes
+#### Bounding Boxes
 
 - Added to the image by clicking and dragging the mouse.
 - Multiple boxes may be added to each image and for each finding.
 - The box is labelled with the name of the last checked checkbox.
 - Moved by clicking and dragging the box. 
 - Deleted by right-clicking on the box and selecting `Remove` from the menu.
 
+#### Radiobuttons
+
+Radiobuttons are stored as integers with the meaning of the integer corresponding to the order of the radiobuttons
+inputted in the configuration wizard. For example, if the radiobuttons are `['Normal', 'Abnormal']`, then the values
+will be `0` for `Normal` and `1` for `Abnormal`.
+
 ### Progress
 
 Your progress through the folder of images is shown in the progress bar at the bottom of the window.
 
-Keyboard Shortcuts
-------------------
+### Keyboard Shortcuts
 
 |                      Key                      |       Action       |
 |:---------------------------------------------:|:------------------:|
@@ -94,6 +114,7 @@ Customisation
 The program can be customised to suit the user's needs. The following options are available:
 - Select which checkboxes are required
 - Select whether checkboxes can be set to 'uncertain' (i.e. 1 - see above)
+- Select whether radiobuttons are required
 - Change the maximum number of backups
 - Backup frequency in minutes
 - Change the backup directory

setup.py

@@ -3,7 +3,7 @@
 setup(
     author='Ian Selby',
     author_email='ias49@cam.ac.uk',
-    description='Tool to label single DICOM images using custom checkboxes',
+    description='Tool to label single DICOM images using custom checkboxes, bounding boxes and radiobuttons',
     name='Speedy QC',
     url='https://github.com/selbs/speedy_qc',
     use_scm_version=True,
@@ -13,7 +13,7 @@
     entry_points={
         'console_scripts': [
             'speedy_qc=speedy_qc.main:main',
-            'speedy_config=speedy_qc.config_wizard:main'
+            'speedy_config=speedy_qc.wizard:main'
         ]
     },
     classifiers=[
@@ -36,6 +36,7 @@
         "setuptools>=42.0.0",
         "python-gdcm>=3.0.21",
         "py2app>=0.28.5",
-        "matplotlib>=3.4.3"
+        "matplotlib>=3.4.3",
+        "imageio>=2.31.0",
     ],
 )

setup_86x64.py

@@ -23,7 +23,7 @@
     entry_points={
         'console_scripts': [
             'speedy_qc=speedy_qc.main:main',
-            'speedy_config=speedy_qc.config_wizard:main'
+            'speedy_config=speedy_qc.wizard:main'
         ]
     },
     classifiers=[
@@ -48,6 +48,7 @@
         "qimage2ndarray>=1.10.0",
         "qt-material>=2.14",
         "QtAwesome>=1.2.3",
-        "matplotlib>=3.4.3"
+        "matplotlib>=3.4.3",
+        "imageio>=2.31.0",
     ],
 )

setup_arm64.py

@@ -25,7 +25,7 @@
     entry_points={
         'console_scripts': [
             'speedy_qc=speedy_qc.main:main',
-            'speedy_config=speedy_qc.config_wizard:main'
+            'speedy_config=speedy_qc.wizard:main'
         ]
     },
     classifiers=[
@@ -50,6 +50,7 @@
         "qimage2ndarray>=1.10.0",
         "qt-material>=2.14",
         "QtAwesome>=1.2.3",
-        "matplotlib>=3.4.3"
+        "matplotlib>=3.4.3",
+        "imageio>=2.31.0",
     ],
 )

speedy_qc/config.yml

@@ -1,21 +1,18 @@
-backup_dir: ~/speedy_qc/backups
+backup_dir: /Users/ianselby/speedy_qc/backups
+backup_interval: 5
 checkboxes:
-- No Finding
-- Enlarged Cardiomediastinum
-- Cardiomegaly
-- Lung Lesion (Mass/Nodule)
-- Airspace Opacity
-- Edema
-- Consolidation
-- Pneumonia
-- Atelectasis / Collapse
-- Pneumothorax / Pneumomediast.
-- Pleural Effusion
-- Pleural Other
-- Fracture
-- Support Devices
-- Other Finding
-log_dir: ~/speedy_qc/logs
-max_backups: 20
-backup_interval: 2
-tristate_cboxes: true
+- QC1
+- QC2
+- QC3
+- QC4
+- QC5
+log_dir: /Users/ianselby/speedy_qc/logs
+max_backups: 10
+radiobuttons:
+- labels:
+  - 1
+  - 2
+  - 3
+  - 4
+  title: Radiobuttons
+tristate_checkboxes: true

speedy_qc/config_chexpert.yml

@@ -0,0 +1,21 @@
+backup_dir: /Users/ianselby/speedy_qc/backups
+backup_interval: 5
+checkboxes:
+- No Finding
+- Enlarged Cardiomediastinum
+- Cardiomegaly
+- Lung Lesion (Mass/Nodule)
+- Airspace Opacity
+- Edema
+- Consolidation
+- Pneumonia
+- Atelectasis / Collapse
+- Pneumothorax / Pneumomediast.
+- Pleural Effusion
+- Pleural Other
+- Fracture
+- Support Devices
+- Other Finding
+log_dir: /Users/ianselby/speedy_qc/logs
+max_backups: 10
+tristate_checkboxes: true

speedy_qc/config_quality.yml

@@ -0,0 +1,35 @@
+backup_dir: /Users/ianselby/speedy_qc/backups
+backup_interval: 5
+log_dir: /Users/ianselby/speedy_qc/logs
+max_backups: 10
+radiobuttons:
+- labels:
+  - Very poor
+  - Poor
+  - Good
+  - Very good
+  title: Overall Quality
+- labels:
+  - Underexposed
+  - Good
+  - Overexposed
+  title: Exposure
+- labels:
+  - Very low
+  - Low
+  - Good
+  - High
+  title: Contrast
+- labels:
+  - None
+  - Mild
+  - Moderate
+  - Severe
+  title: Blur
+- labels:
+  - None
+  - Mild
+  - Moderate
+  - Severe
+  title: Artefacts
+tristate_checkboxes: true