docs: Update README about visualisation of data.

refactor: Revert changes from last commit that alters measurements.

refactor: Update measureSCase() to new method's name.

feat: Updates to work with muscles manual segmentations.

refactor: Correct displayed sentence.

refactor: Update plotSCase() function.

refactor: Update classes in order to work with ShoulderCasePlotter.

refactor: Remove deprecated ShoulderCase plot related functions.

feat: Implement the ShoulderCasePlotter class.

fix: Fix loadAllCases() to actually return the loaded cases.

Merge branch 'boubat' of https://c4science.

refactor: Change properties accessibility to private.

feat: Add class to print updatable message in the command window.

fix: Fix two methods.

refactor: Update and reduce responsability of plotSCase().

refactor: Assert that case is found in loadCase()

refactor: Remove deprecated classes.

refactor: Implement a new ShoulderCaseLoader class.

refactor: Move function to SCaseIDParser class.

feat: Implement plot() method for Glenoid class.

fix: Fix typo.

Merge branch 'boubat'

fix:Scapula: Change the shoulder side selection to load auto landmarks.

refactor:plot: Enhance and update plot functions of classes.

refactor: Update segmentScapula utilisation to new database functions.

refactor: Update segmentScapula utilisation to new database functions.

docs: Correct typos in README.

Merge branch 'boubat'

docs: Update README according to A.Terrier feedback.

build: Remove unused files and folders.

doc: Add file destination in createRotatorCuffSlices().

docs: Implement a whole new README following the costcalc repository model.

refactor:CasesFinder: Change concatenation for fullfile() utilization. Add…

refactor:ShoulderCase: Change reference from auto shoulder to manual shoulder…

docs: Update or add documentation for all classes in ./ShoulderCase.

refactor:CoordinateSystem: Change how the rotationMatrix is created to avoid…

docs:README: Add the description of the config file.

refactor:ShoulderCase: Update objects structure in appendToCSV() and output()…

refactor:measureSCase: Change the creation of SCaseDB variable to take…

docs:README: Update doc.

refactor:measureSCase: Update verification of exisiting muscles data.

refactor:MusclesContainer:createRotatorCuffSlices: Throw an error when there is…

feat:ShoulderCaseLoader: Add a method to load all the cases in the database.

refactor:measureSCase: Replace listSCase() utilisation with ShoulderCaseLoader…

feat:MusclesContainer:clearSummary: Implement the empty state of…

refactor:CoordinateSystem: Extract methods toward Scapula and create the…

perf:cellArraysDifference: Set new algorithm that takes advantage of builtin…

fix:ShoulderCaseLoader: Prevent the error due to outdated SCase call to…

files: Move all the classes in their @Class folder.

refactor:Shoulder: Remove the Muscle addition in Shoulder contructor to prevent…

feat:MusclesContainer: Implement isEmpty() class' method and update other…

refactor: Update system to use new muscles classes.

feat:MusclesContainer:plot: Implement a method that plots segmentation results.

feat:MusclesContainer: Update and move the slicing and segmenting methods here.

refactor:ShoulderCaseLoader: Split the loadCase method into two.

refactor:Muscles: Remove deprecated class Muscles.

refactor:Shoulder:muscles: Update property to new MusclesContainer class.

feat:MuscleMeasurer: Implement new class to measure degeneration related values.

feat:Muscle:measure: Implement the method that replaces Muscles.degeneration.

refactor:MusclesContainer: Change a property type. Add row names to table.

fix:Shoulder: Change shoulder.dataPath not to be set at construction.

doc: Update propagateDataPath function description

fix:paths: Fix errors from the previous commit. Update ShoulderCaseLoader.

feat:Shoulder: Add a dataPath property

feat: Add classes to replace the current Muscles class

build:ShoulderCase: Give the access to ShoulderCase constructor to…

refactor:Muscles: Change property's name

refactor:Muscles:plot: Update files path.

fix:Muscles: Fix typos and errors in new degeneration functions

refactor:Muscles: Extract methods from muscles.degeneration dedicated to the…

refactor:Muscles:newDegeneration: Extract methods that save the results of…

refactor:Muscles:newDegeneration: Extract slicing and segmenting methods from…

feat:Muscles:newDegeneration: Save the image to be segmented in the case's…

refactor:Muscles:newDegeneration: Extract the call to python commands into a…

refactor:Muscles:newDegeneration: Extract a method to clean the rotator cuff…

feat:Muscles: Add a slicedPixelSpacing property.

feat:Muscles:newDegeneration: Add a function to save the slice where it's…

feat:Muscles:plot Implement the plot for this class, displaying the segmented…

refactor:Muscles: Add some properties to prepare the refactoring of Muscles.

refacetor:Muscles:newDegeneration: Sketch the future refactored degeneration…

refactor:DicomVolume: Update and move functions to separate files for the three…

fix:DicomVolumeNormaliser:setMinimalResolutionDividedBy: Prevent the resolution…

feat:DicomVolumeSlicer: Implement the crop() method. Debug ongoing on other…

feat:DicomeVolumeSlicer: Implement the measureSlicedPixelSpacings method

refactor:DicomVolumeNormaliser: Add a division factor to setMinimalResolution().

feat:DicomVolume: Add a method to get the point coordinates given the point…

Merge branch 'Bashardoust_SystCoord'

feat:DicomeVolumeSlicer: Implement the prototype of crop and rotation methods…

perf:Plane:plot: Change the radius argument to be an optional argument

refactor:DicomVolumeNormaliser: Delete deprecated normalising method

perf:Plane:plot: Update the plot method of Plane to show a circle

feat:Circle: Add a Circle object

feat:Plane: Implement the plot method for the PLane class

extract:DicomVolume: Extract methods from DicomeVolumeSlicer class to new…

refactor:Muscles&DicomeVolumeSlicer: Extract the last methods added to the…

feat:Muscles: Add functions to get a slice of a dicom volume

files: Create the @Muscles folder for the Muscles object

feat:ShoulderCaseLoader:loadCase: Add the root path and the dicom path to the…

fix:Shoulder.m:plot: Change the glenoid sphere center for explicit attribution

feat:CoordinateSystem.m: Add a new function to express local coordinates in…