Contributions by Serge X. Cohen

These filters were initially written with X-ray tomographic processing in mind. Still they are of a general usage as long as input are image.

Point-based transformation

Rejecting outliers in 3D

class med-mad-reject

For each pixel of a frame within a stream, makes a 3x3x3 box (that is, 3x3 box including previous, current and following frames) and compute the median (med) and median absolute deviation (mad). If the value of the central pixel is too far from the median (relative to the mad) it is rejected and its value is replaced by the median value of the box.

"threshold": float

When abs(px-med) > threshold*mad the pixel value (noted px) is replaced by med.

Rejecting outliers in 2D

class med-mad-reject-2d

For each pixel of a frame make a square box centred on the pixel and compute the median (med) and median absolute deviation (mad). If the value of the central pixel is too far from the median (relative to the mad) it is rejected and its value is replaced by the median value of the box.

"box-size": uint

The edge size of the box to be used (in px). This should be an even number so that it can be centred on a pixel.

"threshold": float

When abs(px-med) > threshold*mad the pixel value (noted px) is replaced by med.

OpenCL one-liner computation

class ocl-1liner

The aim is to enable the implementation of simple, nevertheless multiple input, computation on the basis of one work-item per pixel of the frame. The filter accepts arbitrary number of inputs, as long as more than one is provided. The output has the same size as the first input (indexed 0) and the generated OpenCL kernel is run with one work item per pixel of the output. The user provides a single computation line and the filter places it within a skeleton to produce an OpenCL kernel on the fly, then compiles it and uses it in the current workflow.

In the kernel the following variables are defined : sizeX and sizeY are the size of the frame in X and Y directions; x and y are the coordinate of the pixel corresponding to the current work item; in_x are the buffer holding the 0..(n-1) input frames; out is the buffer holding the output of the computation.

In the computation line provided through one-line the pixel corresponding to the current work item is px_index. Also reference to the pixel values can use multiple syntax : out[px_index], in_0[px_index], … in_x[px_index] or as shortcut (indeed macro of those) out_px, in_0_px, … in_x_px. Finally if one wants to have finer control over the pixel used in the computation (being able to use neighbouring pixel values) one can use the IMG_VAL macro as such IMG_VAL(x,y,out), IMG_VAL(x,y,in_x) …

"one-line": string

The computation to be performed expressed in one line of OpenCL, no trailing semi-column (added by the skeleton). To avoid miss-interpretation of the symbols by the line parser of ufo-launch it is advisable to surround the line by single quotes (on top of shell quoting). One example (invoking through ufo-launch) would be “‘out_px = (in_0_px > 0) ? sqrt(in_0_px) : 0.0f’” .

"num-inputs": uint

The number of input streams. This is mandatory since it can not be inferred as it is the case by the OpenCL task.

"quiet": boolean

Default to true, when set to false the dynamically generated kernel sources are printed to the standard output during the task setup.

Auxiliary

Producing simple statistics on a stream

class stat-monitor

Inspects a data stream in a way similar to the monitor task but also computing simple statistics on the monitored frame stream: min, max, mean and standard deviation of each frame is computed. To limit truncation errors the OpenCL kernel uses fp64 operations if those are supported by the used OpenCL device, otherwise it falls back to use fp32 arithmetic which might incurs significant truncation errors on images of large dimensions.

"filename": string

When provided the tabulated statistics are output the file with this filename rather than displayed to standard output.

"trace": boolean

When set to true will print processed frame index to standard output. This is useful if the task is placed in before a task somehow hiding the number of processed frames (in a complex workflow). Defaulting to false

"quiet": boolean

When set to true will not print the frame monitoring. Defaulting to false to be as close as possible to the output of the monitor task.

"print": uint

If set print the given numbers of items on stdout as hexadecimally formatted numbers (taken from monitor task).