Add github link and calculation of strain to documentation

CHANGES.md

@@ -1,6 +1,7 @@
 # ChangeLog
 
 ## v25.0.0
+
 Enhancements:
 * Add nexus ".nxs" files reader and converter into raw for the dvc_runner #387
 * Improve `ImageDataCreator` #387
@@ -19,12 +20,13 @@ Bug fixes:
 * Add 3D viewer docking option in the settings #398
 
 Documentation:
+* Add GitHub link #396
+* Add documentation on strain #396
 * Add link to magma dataset and references #426
 
 Dependencies:
 * Add pyside2 and upgrade viewer version #387
 
-
 ## v24.1.1
 Bug fixes:
 * Fix abscissa order in graphs #372

docs/source/index.rst

@@ -6,7 +6,9 @@
 Welcome to iDVC's documentation!
 ================================
 The iDVC app allows a digital volume correlation analysis to be performed on a reference and correlate image volume. You may either use a point cloud you have pre-created, or generate this in the app.
-This manual was written at the time of version 24.1.0 being the latest release.
+This manual was written at the time of version 25.0.0 being the latest release.
+
+GitHub repository: https://tomographicimaging.github.io/iDVC/.
 
 .. toctree::
    :maxdepth: 2
@@ -19,17 +21,8 @@ This manual was written at the time of version 24.1.0 being the latest release.
    saving
    results
    executable
+   strain
    example_datasets
    citations
    references
    contact
-
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

docs/source/strain.rst

@@ -0,0 +1,107 @@
+Strain calculation from the command line
+****************************************
+The strain can be calculated from the command line, within the environment where iDVC is installed. This holds with the full GUI but also for the executable DVC core code. 
+Please note that the latest release does not allow the calculation of the strain from the GUI directly.
+
+The DVC results are saved in the folder "Results", which is generated by running the DVC code, either in the GUI or in the executable. Navigate in the results folder from the command line. 
+Note that this is generated in the GUI only after a session is saved. 
+
+``cd Results`` 
+
+From this folder, in the terminal, type
+
+``strain  dvc_result_0.disp``
+
+where the result file ending with ".disp" could have a different name in a bulk run.
+This command creates 2 strain output files calculated from the displacement file: "dvc_result_0.sort.csv" and "dvc_result_0-sw25.Lstr.csv". 
+The following fields are included in the latter.
+
+``n``
+   Index of the subvolume or point.
+
+``x``, ``y``, ``z``
+   Coordinates of the center of the subvolume (in voxels units).
+
+``u_fit``
+   Displacement in the x-direction.
+
+``v_fit``
+   Displacement in the y-direction.
+
+``w_fit``
+   Displacement in the z-direction.
+
+``pts_in_sw``
+   Number of points in the subvolume.
+
+``sw_radius``
+   Radius (half-size) of the subvolume used for correlation (in voxels).
+
+``exx``
+   Normal strain in the x-direction (∂u/∂x).
+
+``eyy``
+   Normal strain in the y-direction (∂v/∂y).
+
+``ezz``
+   Normal strain in the z-direction (∂w/∂z).
+
+``exy``
+   Shear strain in the xy-plane (½(∂u/∂y + ∂v/∂x)).
+
+``eyz``
+   Shear strain in the yz-plane (½(∂v/∂z + ∂w/∂y)).
+
+``exz``
+   Shear strain in the xz-plane (½(∂u/∂z + ∂w/∂x)).
+
+``ep1``
+   First principal strain (maximum eigenvalue of the strain tensor).
+
+``ep2``
+   Second principal strain (middle eigenvalue of the strain tensor).
+
+``ep3``
+   Third principal strain (minimum eigenvalue of the strain tensor).
+
+
+Help information
+================
+
+Type ```strain``` on the command line to generate the following help information
+
+strain dvc.disp.csv
+
+- use dvc output file dvc.disp.csv, create sort file, use default run settings
+- it is much more efficient to read an existing .sort file, particularly for large point clouds
+- strain will run with only a .disp file, creating a .sort file in the process for subsequent use
+
+strain dvc.disp.csv dvc.sort.csv
+
+- use dvc output file dvc.disp.csv and sort file dvc.sort.csv, use default run settings
+- use either a .sort file created during the dvc run or one created during an initial strain run
+
+Default settings:
+
+strain window = 25 points (min = 10, max = 75)
+
+- reset with -sw flag
+
+objmin threshold = 1 (min = 0.0001, max = 1)
+
+-  values lower than the threshold are used in filling the strain window
+- the default value of 1.0 passes all convergent points into the strain window
+- reset with -t flag
+
+output Lagrangian strain values
+
+- adjust output with -E, -D, and -A flags
+
+Command line flags: 
+
+- -sw 30 specify a target number of points for the strain windows (e.g. 30) 
+- -t 0.01 specify the objmin threshold value (e.g. 0.01)
+- -r refill strain window with points passing threshold (may expand strain window size)
+- -E add engineering strain output (default is Lagrangian)
+- -D add displacement gradient tensor output
+- -A write all output files