From 0445093d904d394d16c940999ff98e17acdc4406 Mon Sep 17 00:00:00 2001 From: Danica Sugic Date: Tue, 22 Apr 2025 16:03:58 +0100 Subject: [PATCH 1/8] Edit documentation --- CHANGES.md | 4 ++++ docs/source/index.rst | 14 +++----------- 2 files changed, 7 insertions(+), 11 deletions(-) diff --git a/CHANGES.md b/CHANGES.md index 27e13499..2092c45d 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,5 +1,9 @@ # ChangeLog +## v24.x.x +Documentation: +* Add GitHub link # + ## v24.1.1 Bug fixes: * Fix abscissa order in graphs #372 diff --git a/docs/source/index.rst b/docs/source/index.rst index 00a6395d..b8f32d89 100644 --- a/docs/source/index.rst +++ b/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 24.1.1 being the latest release. + +GitHub repository: https://tomographicimaging.github.io/iDVC/. .. toctree:: :maxdepth: 2 @@ -21,13 +23,3 @@ This manual was written at the time of version 24.1.0 being the latest release. executable citations contact - - - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` From 20d7f4edfa8ff7ad85004e384e49932d4ddacf3d Mon Sep 17 00:00:00 2001 From: Danica Sugic Date: Tue, 22 Apr 2025 16:05:58 +0100 Subject: [PATCH 2/8] Add pr number --- CHANGES.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGES.md b/CHANGES.md index 2092c45d..958f9907 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -2,7 +2,7 @@ ## v24.x.x Documentation: -* Add GitHub link # +* Add GitHub link #396 ## v24.1.1 Bug fixes: From 9008bbc913455f317449bf0636bfcdbd934df929 Mon Sep 17 00:00:00 2001 From: Danica Sugic Date: Tue, 22 Apr 2025 16:49:31 +0100 Subject: [PATCH 3/8] Add strain documentation--partial --- docs/source/index.rst | 1 + docs/source/strain.rst | 25 +++++++++++++++++++++++++ 2 files changed, 26 insertions(+) create mode 100644 docs/source/strain.rst diff --git a/docs/source/index.rst b/docs/source/index.rst index b8f32d89..9aab6d63 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -21,5 +21,6 @@ GitHub repository: https://tomographicimaging.github.io/iDVC/. saving results executable + strain citations contact diff --git a/docs/source/strain.rst b/docs/source/strain.rst new file mode 100644 index 00000000..d3c7f03e --- /dev/null +++ b/docs/source/strain.rst @@ -0,0 +1,25 @@ +Calculate the strain +************** +Whether you have installed the full gui, or just the executable, you are able to calculate the strain from the command line, in the environment where you have installed it. +Please note that the latest release does not allow the calculation of the strain in the GUI, this needs to be implemented in the command line. + +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`` + +This command creates 2 files with strain results calculated from the displacement file. + +dvc_result_0.sort.csv + +... + +dvc_result_0-sw25.Lstr.csv + +... +n x y z u_fit v_fit w_fit pts_in_sw sw_radius exx eyy ezz exy eyz exz ep1 ep2 ep3 + From b3a015d58752cabe6f28e7a88289428dbed2e92f Mon Sep 17 00:00:00 2001 From: Danica Sugic Date: Wed, 2 Jul 2025 11:52:17 +0100 Subject: [PATCH 4/8] modify strain documentation --- docs/source/strain.rst | 41 +++++++++++++++++++++++++++++++++++++++-- 1 file changed, 39 insertions(+), 2 deletions(-) diff --git a/docs/source/strain.rst b/docs/source/strain.rst index d3c7f03e..75db91e1 100644 --- a/docs/source/strain.rst +++ b/docs/source/strain.rst @@ -1,5 +1,5 @@ -Calculate the strain -************** +Strain calculation from the command line +**************************************** Whether you have installed the full gui, or just the executable, you are able to calculate the strain from the command line, in the environment where you have installed it. Please note that the latest release does not allow the calculation of the strain in the GUI, this needs to be implemented in the command line. @@ -23,3 +23,40 @@ dvc_result_0-sw25.Lstr.csv ... n x y z u_fit v_fit w_fit pts_in_sw sw_radius exx eyy ezz exy eyz exz ep1 ep2 ep3 +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 \ No newline at end of file From 9e081845a07b2df10bd15198321e14becc74cf96 Mon Sep 17 00:00:00 2001 From: Danica Sugic Date: Wed, 2 Jul 2025 15:21:21 +0100 Subject: [PATCH 5/8] Edit strain file --- docs/source/strain.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/source/strain.rst b/docs/source/strain.rst index 75db91e1..065eb345 100644 --- a/docs/source/strain.rst +++ b/docs/source/strain.rst @@ -23,6 +23,8 @@ dvc_result_0-sw25.Lstr.csv ... n x y z u_fit v_fit w_fit pts_in_sw sw_radius exx eyy ezz exy eyz exz ep1 ep2 ep3 +**Help information** + Type ```strain``` on the command line to generate the following help information strain dvc.disp.csv @@ -36,7 +38,7 @@ 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:** +Default settings: strain window = 25 points (min = 10, max = 75) From 013233014456490bbdab5defdde7461eb19fd260 Mon Sep 17 00:00:00 2001 From: Danica Sugic Date: Wed, 2 Jul 2025 15:22:59 +0100 Subject: [PATCH 6/8] Edit changelog --- CHANGES.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGES.md b/CHANGES.md index 958f9907..fa6e86cb 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,8 +1,9 @@ # ChangeLog -## v24.x.x +## v25.0.0 Documentation: * Add GitHub link #396 +* Add documentation on strain #396 ## v24.1.1 Bug fixes: From 6b73c02c8685dfe59549d5ea52e387a4ea8da6a7 Mon Sep 17 00:00:00 2001 From: Danica Sugic Date: Tue, 15 Jul 2025 14:43:38 +0100 Subject: [PATCH 7/8] edit strain file --- docs/source/strain.rst | 61 +++++++++++++++++++++++++++++++++++------- 1 file changed, 52 insertions(+), 9 deletions(-) diff --git a/docs/source/strain.rst b/docs/source/strain.rst index 065eb345..f6c95d4e 100644 --- a/docs/source/strain.rst +++ b/docs/source/strain.rst @@ -1,7 +1,7 @@ Strain calculation from the command line **************************************** -Whether you have installed the full gui, or just the executable, you are able to calculate the strain from the command line, in the environment where you have installed it. -Please note that the latest release does not allow the calculation of the strain in the GUI, this needs to be implemented in 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. @@ -12,18 +12,61 @@ From this folder, in the terminal, type ``strain dvc_result_0.disp`` -This command creates 2 files with strain results calculated from the displacement file. +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. -dvc_result_0.sort.csv +``n`` + Index of the subvolume or point. -... +``x``, ``y``, ``z`` + Coordinates of the center of the subvolume (in voxels units). -dvc_result_0-sw25.Lstr.csv +``u_fit`` + Displacement in the x-direction. -... -n x y z u_fit v_fit w_fit pts_in_sw sw_radius exx eyy ezz exy eyz exz ep1 ep2 ep3 +``v_fit`` + Displacement in the y-direction. -**Help information** +``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 From 27d495ada9b20cf558af349b1b226f3b59b36e33 Mon Sep 17 00:00:00 2001 From: Danica Sugic Date: Tue, 15 Jul 2025 14:54:43 +0100 Subject: [PATCH 8/8] edit version number in documentation --- docs/source/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index 145c8ff3..56dc8dc0 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -6,7 +6,7 @@ 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 24.1.1 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/.