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Commit b294c250 authored by Edward Andò's avatar Edward Andò
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Resolved #170 (doc issue)

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......@@ -36,7 +36,7 @@ for speed.
Some user-callable scipts are also provided -- they are more
complex pieces of code that combine a number of functions and
which have a command-line interface.
For the moment the clients are 3 different image correlation
For the moment the scripts are 3 different image correlation
techniques.
Please have a look at our online documentation for:
......
......@@ -53,6 +53,7 @@ Here's a list of existing **spam** scripts organised into categories:
- **spam-ddic** — Discrete image correlation with discrete objects defined with labelled image see: :ref:`discreteDICscript`
- **spam-moveGrains** — Deform a labelled image with displacements defined for each label
- **spam-discreteStrain** — Computes strains on a tetrahedral mesh linking grain centres
- **spam-ereg-discrete** — A graphical tool to pre-align grains for correlation
Description of image correlation scripts
#########################################
......@@ -90,8 +91,7 @@ This script can **run in parallel** using the MPI multiprocessing library by put
Other key input options are (check figure below for illustration):
- *-ns* and *-hws* set the spacing between the grid points in pixels and the "half window size" in pixels. Since measurements are defined as centred on a point, the subvolume which is extracted from around the point is "half window size" pixels on each size of the central point, yielding a volume 1+2*hws in each direction.
- *-reg* performs an initial registration of the two provided images -- **this is highly recommended**. In many cases (without too complicated and large displacement fields), this step can avoid the need to perform a computationally expensive pixel search. The option *-regb* bins (downscales by a given factor) the entire input images to save time.
- *-glt* and *-ght* **prevent** a correlation from occurring if the mean greyvalue of the extracted subvolume is less than *glt* or higher than *ght*.
- *-regbb* and *-regbe* to perform an *initial multiscale registration* of the two provided images -- **this is highly recommended**. In many cases (without too complicated and large displacement fields), this step can avoid the need to perform a computationally expensive pixel search. *-regbb* defines the initial binning level *-regbe* defines the final binning level. - *-glt* and *-ght* **prevent** a correlation from occurring if the mean greyvalue of the extracted subvolume is less than *glt* or higher than *ght*.
- *-gpi* and *-gpp* regulate convergence options for each grid point `spam.DIC.register` run in a subvolume: the number of maximum iterations and the smallest change in the norm of Φ (:math:`\delta\Phi_{min}`) respectively.
- *-od* and *-pre* set the output directory and the prefix for the output files respectively.
......@@ -145,9 +145,9 @@ The code will return, for each measurement point/node (thus the centre of correl
- The point's number
- The point's Z,Y,X position
- The point's Z,Y,X displacement
- The subvolume's components of Φ matrix
- The error for this subvolume: final difference in greylevels between im1 and im2(:math:`\Phi`.x) subvolumes with a normalisation applied.
- The measured point's Z,Y,X displacement
- The measured subvolume's components of F matrix
- The correlation error for this subvolume: final difference in greylevels between im1 and im2(:math:`\Phi`.x) subvolumes with a normalisation applied.
- The number of iterations until convergence (equal to *-gpi* if convergence was not reached)
- The return status (**this is important!**):
......@@ -216,9 +216,9 @@ Here is an example of the vertical slices through the "Martian Simulant" M2EA05
Other key input options are:
- *-ld* sets how many iterations of dilation will be applied to each object to extract the greylevels to correlate
- *-reg* performs an initial registration of the two provided images -- **this is highly recommended**. In many cases (without too complicated and large displacement fields), this step can avoid the need to perform a computationally expensive pixel search. The option *-regb* bins (downscales by a given factor) the entire input images to save time.
- *-regbb* and *-regbe* to perform an *initial multiscale registration* of the two provided images -- **this is highly recommended**. In many cases (without too complicated and large displacement fields), this step can avoid the need to perform a computationally expensive pixel search. *-regbb* defines the initial binning level *-regbe* defines the final binning level.
- *-vt* the volume (in voxels) of the smallest object to correlate.
- *-gpi* and *-gpp* regulate convergence options for each grid point `spam.DIC.correlate.register` run in an object: the number of maximum iterations and the smallest change in the norm of Φ (:math:`\delta\Phi_{min}`) respectively.
- *-lci* and *-lcp* regulate convergence options for each grid point `spam.DIC.correlate.register` run in an object: the number of maximum iterations and the smallest change in the norm of Φ (:math:`\delta\Phi_{min}`) respectively.
- *-od* and *-pre* set the output directory and the prefix for the output files respectively.
As per the ``spam-ldic`` script, a large number of other options exist and can be seen with **- -help**.
......@@ -234,6 +234,27 @@ By default the outputs of a discrete correlation are:
- a TSV file with the transformation and correlation status for each object
- a VTK file with the displacement vectors of each object
The code will return, for each label, the following information:
- The label number
- The label's Z,Y,X position (centre of mass)
- The measured label's Z,Y,X displacement
- The measured label's components of F matrix
- The correlation error for this label: final difference in greylevels between im1 and im2(:math:`\Phi`.x) subvolumes with a normalisation applied.
- The number of iterations until convergence (equal to *-lci* if convergence was not reached)
- The return status (**this is important!**):
- 2 = **Convergence**: reached desired :math:`\delta\Phi_{min}` (*-lcp* input)
- 1 = **Not Convergence**: stopped by hitting the maximum number of iterations (*-lci* input) without diverging
- -1 = **Divergence**: error is more than 80% of previous iteration error (see `spam.DIC.correlate.register`)
- -2 = Iterative procedure stopped: singular matrix M cannot be inverted (see `spam.DIC.correlate.register`)
- -3 = Divergence: diverged on displacement or volumetric change condition (see `spam.DIC.correlate.register`)
- -4 = Margin alignment for im1 and im2 subvolumes failed (the iterative procedure never started)
- -5 = Failed margin alignment (too close to edge?) or failed volume condition
- -6 = Not used right now
- -7 = Label missing or NaNs/infinite in Phi
As per ``spam-ldic`` script, to perform a discrete correlation between these two M2EA05 states, again only very simple lines are needed:
.. code-block:: console
......
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