Reads data from the align & average step and provides a GUI which is essentially a wrapper for Scipy's FITPACK bivariate spline fitting function. Writes to a results *.mat file containing the spline fit both from FITPACK as well as attempting to match MATLAB's spline objects.
Input and output descriptors
| Input | Description |
|---|---|
| Input file | A *.mat file with a ref structure containing an x_out field, see point_cloud: Nx3 matrix of the points that comprise the outline, and a matrix aa, which is an Nx3 matrix of points comprising the aligned and averaged data - see align_average. |
| Output | Description |
|---|---|
| Spline data structure | A spline_x structure written to the *.mat results file which contains the following fields:
|
| Averaged point cloud mask | 1xN array of int8 values called aa_mask consisting of 0 and 1 where 0 indicates a masked point. Conversion to a boolean array will provide an index of aligned and averaged point cloud that were masked (e.g. not used) for the fitted spline. |
The function can be called from interactive Python, for example:
>>>from pyCM import fit_surface as fs
>>>fs.sf_def()
which will provide a GUI to locate the *.mat file with the necessary data according to the description above. Alternatively, the path to the target *.mat file can be specified directly:
>>>from pyCM import fit_surface as fs
>>>fs.sf_def('PathToMatFile.mat')
On launching, a custom interactor is generated (Fig. 1) which permits the same types of manipulation as other pyCM tools in terms of view manipulation. The z, x and c keys only affect the view aspect in the z direction, however.
Figure 1: Loaded data with the reference outline and aligned and averaged data set shown, along with masked data also displayed.
If artefacts from averaging are present, these can be manually removed with the same interaction employed in point_cloud. This function should be used sparingly, but can be used to make minor changes on edges of samples which might contain wire entry/exit artefacts.
For fitting, the user has access to the main arguments of the scipy.interpolate.bisplrep function via input boxes. Pressing the Update button will both fit and display the result based on the selected parameters. The Display resolution pane permits the user to view the fit of the spline with a higher resolution, and ensure that the point cloud is effectively fitted in all areas. By default, the display resolution is set to half of the knot spacing in either x and y directions.
For further examination of the fit in all locations of the point cloud, the spline/point cloud can be sectioned, by using the Data sectioning pane. An example of this is shown in Fig. 2. This can be done as many times as needed, the Revert button will undo all sectioning.
Figure 3: Sectioned spline compared to the point cloud.
Pressing the 'Write' button will update the *.mat file with the result of the spline. Another file or a revision of fitting can be conducted by pressing l
Keyboard and mouse mapping
| Key | Description |
|---|---|
| Left mouse button | Rotate about the center of view |
| Middle mouse button | Pan |
| Right mouse button | Zoom/refresh window extents |
| 1 | View 1, default, looks down z axis onto xy plane |
| 2 | View 2, default, looks down x axis onto zy plane |
| 3 | View 3, default, looks down y axis onto zx plane |
| z | increase z-aspect ratio |
| x | decrease z-aspect ratio |
| c | return to default z-aspect |
| f | flip colors from white on dark to dark on white |
| i | save output to spline_fit.png in current working directory |
| r | remove/reinstate compass/axes |
| o | remove/reinstate outline |
| l | load/reload *.mat file |
None at this time.