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Commit e9d53685 authored by Olga Stamati's avatar Olga Stamati
Browse files

filter field docs

parent 13c8f74e
Pipeline #66116 passed with stages
in 13 minutes and 47 seconds
......@@ -8,10 +8,10 @@ digraph G {
DEF [label="spam-deformImage", color="#c46747", fillcolor="#FFEAE6", style="bold, filled", shape=ellipse, href="#pixel-search-script-spam-pixelsearch", target="_top"];
REG [label="spam-reg", color="#c46747", fillcolor="#FFEAE6", style="bold, filled", shape=ellipse, href="#registration-script-spam-reg", target="_top"];
PS [label="spam-pixelSearch", color="#c46747", fillcolor="#FFEAE6", style="bold, filled", shape=ellipse, href="#pixel-search-script-spam-pixelsearch", target="_top"];
LDIC [label="spam-ldic", color="#c46747", fillcolor="#FFEAE6", style="bold, filled", shape=ellipse, href="#regular-grid-local-dic-script-spam-ldic", target="_top"];
FILT [label="spam-filterPhiField", color="#c46747", fillcolor="#FFEAE6", style="bold, filled", shape=ellipse, href="#filtering-script-spam-filterphifield", target="_top"];
LDIC [label="spam-ldic", color="#c46747", fillcolor="#FFEAE6", style="bold, filled", shape=ellipse, href="#regular-grid-local-dic-script-spam-ldic", target="_top"];
//PASS [label="spam-passPhiField", color="#c46747", fillcolor="#FFEAE6", style="bold, filled", shape=ellipse, href="#regular-grid-local-dic-script-spam-ldic", target="_top"];
FILT [label="spam-filterPhiField", color="#c46747", fillcolor="#FFEAE6", style="bold, filled", shape=ellipse, href="#filtering-script-spam-filterPhiField", target="_top"];
STR [label="spam-regularStrain", color="#c46747", fillcolor="#FFEAE6", style="bold, filled", shape=ellipse, href="#regular-strain-script-spam-regularStrain", target="_top"];
STR [label="spam-regularStrain", color="#c46747", fillcolor="#FFEAE6", style="bold, filled", shape=ellipse, href="#regular-strain-script-spam-regularstrain", target="_top"];
// questions
QEREG [shape=box, label="misaligned images?"];
......@@ -46,7 +46,7 @@ digraph G {
REG -> REGR[label="Converged?"];
//REGR -> RES;
REGR -> DEF;
DEF -> RES;
//DEF -> RES;
REGR -> PS[style=dashed, color="#c46747"];
REGR -> LDIC[style=dashed, color="#c46747"];
......@@ -55,16 +55,18 @@ digraph G {
PS -> PSR[label="High CC?"];
//PSR -> RES;
PSR -> DEF//[constraint=false];
DEF -> RES;
//DEF -> RES;
PSR -> QFILT;
PSR -> LDIC[style=dashed, color="#c46747"];
// filter ps
// ldic
LDICR [label="keep Φ field", shape=note, margin=0];
LDIC -> LDICR;
LDICR -> DEF//[constraint=false];
DEF -> RES;
//DEF -> RES;
// filter
// filter ldic
LDICR -> QFILT;
FILT -> STR;
......
......@@ -95,7 +95,7 @@ The result of this eye-alignment is a **single** Φ (linear and homogeneous defo
``Input:``
.........
.............
**Required**
......@@ -108,7 +108,7 @@ The result of this eye-alignment is a **single** Φ (linear and homogeneous defo
.. HINT:: Make sure that the format of this file is compatible with a spam-style correlation file. (Run, for example, this script and check the result)
``Output:``
.........
.............
- A *".tsv"* file containing:
......@@ -194,7 +194,7 @@ It measures a **single** Φ (linear and homogeneous deformation function, see :r
.. _here: https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/DIC.html#DIC.correlate.registerMultiscale
``Input:``
.........
.............
**Required**
......@@ -223,7 +223,7 @@ It measures a **single** Φ (linear and homogeneous deformation function, see :r
- ``-def``: Ask to **save** the **deformed** im1 at the end of the iterative algorithm. This is the measured Φ applied to im1
``Output:``
.........
.............
- A *".tsv"* file containing:
......@@ -301,7 +301,7 @@ It measures a **displacement field** with a **1-pixel sensitivity** that maps im
2. **Discrete** points. For example centres of mass of particles, if your objective is to perform particle tracking. See :ref:`labelToolkitTutorial` for more information. This mode is activated with ``-lab1`` input option
``Input:``
.........
.............
**Required**
......@@ -342,7 +342,7 @@ It measures a **displacement field** with a **1-pixel sensitivity** that maps im
``Output:``
.........
.............
- A *".tsv"* file containing:
......@@ -361,7 +361,7 @@ For the **structured grid** mode, the script can be run like this:
$ source /path/to/spam/venv/bin/activate
(spam) $ spam-pixelSearch \ # the script
/path/to/my/data/im1.tif /path/to/my/data/im2.tif \ # the two 3D or 2D images (tiff files) to correlate
-mf1 /path/to/my/data/im1.tif -mc 0.5 \ # the mask of im1, and the coverage to skip the subvolumes
-mf1 /path/to/my/data/mask1.tif -mc 0.5 \ # the mask of im1 and the coverage to skip the subvolumes
-pf /path/to/my/data/initialPhi.tsv -pfb 2 \ # initial guess, which was run in half-sized images
-ns X -hws X \ # node spacing and half window size of the grid
-sr -Z Z -Y Y -X X \ # search range
......@@ -413,7 +413,7 @@ It measures a **displacement field** with a **1-pixel sensitivity** that maps im
- There are **large** and **not homogeneous** deformations between the two configurations and
- The **texture** of the material is **weak**
Such a challeging case could look like this:
Such a challenging case could look like this:
.. figure:: images/tutorial/scripts/psPropInput.png
:align: center
......@@ -443,7 +443,7 @@ It measures a **displacement field** with a **1-pixel sensitivity** that maps im
This means that this script can **not** run **in parallel**.
``Input:``
.........
.............
**Required**
......@@ -486,7 +486,7 @@ It measures a **displacement field** with a **1-pixel sensitivity** that maps im
``Output:``
.........
.............
- A *".tsv"* file containing:
......@@ -592,7 +592,7 @@ It measures a **field of deformation functions** that map each subvolume in im1
.. _function: https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/DIC.html#DIC.correlate.register
``Input:``
.........
.............
**Required**
......@@ -624,7 +624,7 @@ It measures a **field of deformation functions** that map each subvolume in im1
- ``-tif``: Ask for a tif **output** for **visualisation** of the displacement and the iterative algorithm information fields
``Output:``
.........
.............
- A *".tsv"* file containing:
......@@ -707,7 +707,7 @@ This script facilitates the manipulation of different Φ fields, applying a sing
In both cases, you can choose which part of Φ (see :ref:`imageCorrelationTheory`) will be passed setting the input option ``-m``.
``Input:``
.........
.............
**Required**
......@@ -742,10 +742,11 @@ This script facilitates the manipulation of different Φ fields, applying a sing
- ``-lab1`` The labelled image (see :ref:`labelToolkitTutorial`) from which the **output positions** are calculated (centres of mass of labels)
``Output:``
.........
.............
- A *".tsv"* file containing:
- A *".tsv"* file of the deformation field defined at the **new positions**:
- New points **position** (Z, Y, X), as defined by the input grid (``-ns``) or the labelled image (``-lab1``)
- New **positions** (Z, Y, X), as defined by the input grid (``-ns``) or the labelled image (``-lab1``)
- The components of the applied or interpolated deformation function (*Fzz*, *Fzy*, *Fzx*, *Zdisp*, *etc*). Option ``-m`` defined which part of Φ was passed
- For compatibility reasons, information related to the iterative algorithm in ``spam.DIC.register()`` (*iterations*, *error*, *deltaPhiNorm*, *returnStatus*). These are **totally irrelevant** to the result of this script
......@@ -805,29 +806,36 @@ This script corrects/filters a deformation field.
It is **recommended** to use this script **before** calculating **strains**.
.. IMPORTANT::
This script **selects bad points** based on:
This script **selects bad points** based on a **threshold** on:
- the **correlation coefficient**, activated with. A point's correlation coefficient is the result of :ref:`pixelSearch`, :ref:`pixelSearchPropagate`. Typically a coefficient **greater** than 0.9 is a good threshold
- the **return status**, activated with. A point's return status is the result of :ref:`ldic`, :ref:`ddic`. A return status of 2 means that the local algorithm has converged
- the **local coherency**, activated with. A point's local coherency is the average residual between the point's displacement and a second-order parabolic surface, fitted to the point's closest N neighbours and evaluated at the point's position. Typically, a point with a coherency value **smaller** than 0.1 is classified as coherent
- the *returnStatus* of the correlation algorithm, activated with
- the *local coherency value*, activated with
This script **corrects bad points** based on:
- inverse distance weighting of closest (``-nr`` or ``-nn``) good neighbours, activated with
- gaussian distance weighting of closest (``-nr`` or ``-nn``) good neighbours, activated with
- inverse distance weighting of closest good neighbours, activated with
- gaussian distance weighting of closest good neighbours, activated with
- local quadratic fit of closest good neighbours, activated with
Closest neighbours are selected based on distance ``-nr`` or number ``-nn``.
This script **filters bad points** based on:
- mean of closest neighbours
- median filter
This script **ignores background points** based on a **threshold** on:
- the *return status*, activated with. The return status coefficient is the result of
``Input:``
.........
.............
**Required**
- *-pf*: *".tsv"* file containing the deformation **field**. This file can come either from :ref:`pixelSearch`, :ref:`pixelSearchPropagate`, :ref:`ldic` or :ref:`passPhi`
- ``-pf``: *".tsv"* file containing the deformation **field**. This file can come either from :ref:`pixelSearch`, :ref:`pixelSearchPropagate`, :ref:`ldic` or :ref:`passPhi`
**Optional**
......@@ -841,10 +849,11 @@ This script corrects/filters a deformation field.
``Output:``
.........
.............
- A *".tsv"* file defined at the **same** points as the input field:
- A *".tsv"* file containing:
- The points position (Z, Y, X) which are the **same** as the **input** field
- Deformation functions and information related to the iterative algorithm status (*returnStatus*, *iterations*, *etc*) of **points** defined as **good** are **not modified**
- Deformation functions of **points** defined as **bad** are **modified** based on the application asked
- *returnStatus* of **points** defined as **bad** is **modified** (*returnsStatus* = 1)
......@@ -892,7 +901,7 @@ This scripts calculates the strain field between im1 and im2, based on a displac
For further details regarding the strain calculation in spam and the output of this script please see the detailed tutorial here :ref:`strainTutorial`.
``Input:``
.........
.............
**Required**
......@@ -909,7 +918,7 @@ This scripts calculates the strain field between im1 and im2, based on a displac
- ``-tif``: Ask for a tif output for **visualisation** of the strain field
``Output:``
.........
.............
- A *".tsv"* file containing:
......
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