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Commit 5d0dee2f authored by David Hammer's avatar David Hammer
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Add peak min / max pixels threshold, add a bunch of descriptions

parent 61f8ea94
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2 merge requests!151Draft: PF9 compact output,!150PF9 with threshold on min/max pixels in peak
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src/calng/correction_addons/peakfinder9.py
+ 69
− 0
View file @ 5d0dee2f
......@@ -17,6 +17,17 @@ class Peakfinder9(BaseCorrectionAddon):
(
UINT32_ELEMENT(schema)
.key(f"{prefix}.windowRadius")
.description(
"The algorithm works by first deciding (in parallel, looking at each "
"pixel) if 'current pixel' is a candidate as start of a peak. Then, it "
"moves out in rings, expanding peak up until at most windowRadius. "
"The border of the window is used for background estimation. The other "
"parameters adjust rejection criteria for the 'current pixel' "
"(minPeakValueOverNeighbors, minSnrMaxPixel), criteria for adding "
"pixels to the peak (minSnrPeakPixels), and rejection criteria for the "
"full peak after expansion (minSnrWholePeak, minPeakPixels, "
"maxPeakPixels)."
)
.tags("managed")
.assignmentOptional()
.defaultValue(2)
......@@ -25,6 +36,10 @@ class Peakfinder9(BaseCorrectionAddon):
UINT32_ELEMENT(schema)
.key(f"{prefix}.maxPeaks")
.description(
"For GPU buffer reasons, we need an upper limit on how many peaks "
"there will be per frame. Just leave this reasonably high."
)
.tags("managed")
.assignmentOptional()
.defaultValue(500)
......@@ -33,6 +48,11 @@ class Peakfinder9(BaseCorrectionAddon):
FLOAT_ELEMENT(schema)
.key(f"{prefix}.minPeakValueOverNeighbors")
.description(
"Current pixel is rejected as start of peak if it does not exceed the "
"maximum pixel value on the window border by at least this amount; "
"note, this is in absolute terms unlike other parameters."
)
.tags("managed")
.assignmentOptional()
.defaultValue(10)
......@@ -41,6 +61,11 @@ class Peakfinder9(BaseCorrectionAddon):
FLOAT_ELEMENT(schema)
.key(f"{prefix}.minSnrMaxPixel")
.description(
"Current pixel is rejected as start of peak if it does not exceed mean "
"by at least mean by this amount times sigma. Both mean and sigma are "
"based on window border pixels."
)
.tags("managed")
.assignmentOptional()
.defaultValue(5)
......@@ -49,6 +74,12 @@ class Peakfinder9(BaseCorrectionAddon):
FLOAT_ELEMENT(schema)
.key(f"{prefix}.minSnrPeakPixels")
.description(
"If current pixel was not rejected until now, we start expanding peak "
"layer by layer. For a pixel to be added to the peak, it must (be in "
"the next layer, and) exceed the mean by at least this number times "
"sigma."
)
.tags("managed")
.assignmentOptional()
.defaultValue(4)
......@@ -57,14 +88,47 @@ class Peakfinder9(BaseCorrectionAddon):
FLOAT_ELEMENT(schema)
.key(f"{prefix}.minSnrWholePeak")
.description(
"After expanding peak with additional peak pixels, the whole peak is "
"rejected if its total mass does not exceed the mean by at least this "
"number times sigma."
)
.tags("managed")
.assignmentOptional()
.defaultValue(6)
.reconfigurable()
.commit(),
UINT32_ELEMENT(schema)
.key(f"{prefix}.minPeakPixels")
.description(
"After expanding peak, it is rejected if the number of pixels is not "
"at least this."
)
.tags("managed")
.assignmentOptional()
.defaultValue(1)
.reconfigurable()
.commit(),
UINT32_ELEMENT(schema)
.key(f"{prefix}.maxPeakPixels")
.description(
"After expanding peak, it is rejected if the number of pixels exceeds "
"this."
)
.tags("managed")
.assignmentOptional()
.defaultValue(100)
.reconfigurable()
.commit(),
FLOAT_ELEMENT(schema)
.key(f"{prefix}.minSigma")
.description(
"When background estimate for stdev is very low, this is used to set "
"minimum sigma value used for the thresholds above."
)
.tags("managed")
.assignmentOptional()
.defaultValue(5)
......@@ -73,6 +137,7 @@ class Peakfinder9(BaseCorrectionAddon):
UINT32_ELEMENT(schema)
.key(f"{prefix}.blockX")
.description("GPU execution tuning parameter you probably want to ignore.")
.tags("managed")
.assignmentOptional()
.defaultValue(1)
......@@ -81,6 +146,7 @@ class Peakfinder9(BaseCorrectionAddon):
UINT32_ELEMENT(schema)
.key(f"{prefix}.blockY")
.description("GPU execution tuning parameter you probably want to ignore.")
.tags("managed")
.assignmentOptional()
.defaultValue(1)
......@@ -89,6 +155,7 @@ class Peakfinder9(BaseCorrectionAddon):
UINT32_ELEMENT(schema)
.key(f"{prefix}.blockZ")
.description("GPU execution tuning parameter you probably want to ignore.")
.tags("managed")
.assignmentOptional()
.defaultValue(64)
......@@ -214,6 +281,8 @@ class Peakfinder9(BaseCorrectionAddon):
cupy.float32(self._config["minSnrPeakPixels"]),
cupy.float32(self._config["minSnrWholePeak"]),
cupy.float32(self._config["minSigma"]),
cupy.uint32(self._config["minPeakPixels"]),
cupy.uint32(self._config["maxPeakPixels"]),
cupy.uint32(self._config["maxPeaks"]),
)
......
src/calng/kernels/peakfinder9_gpu.cu
+ 31
− 27
View file @ 5d0dee2f
......@@ -58,14 +58,19 @@ public:
extern "C" __global__ void pf9(const unsigned short num_frames,
const unsigned short ss_dim,
const unsigned short fs_dim,
const unsigned short window_radius,
const float min_peak_over_border,
const float min_snr_biggest_pixel,
const float min_snr_peak_pixels,
const float min_snr_whole_peak,
const float min_sigma,
const unsigned int max_peaks,
const float* image,
const unsigned short window_radius, // radius to border: border is for background estimate and bounds peak size
const float min_peak_over_border, // for "current pixel" to be candidate, it must be this much (absolute value) over max value on border
// for the next parameters, snr is based on stdev of border pixels
// note: hardcoded limit says there must be at least 10 non-masked border pixels for this
const float min_snr_biggest_pixel, // "current pixel" is compared against this
// we "expand" peak in rings
const float min_snr_peak_pixels, // additional peak pixels get compared against this
const float min_snr_whole_peak, // total mass of peak after expansion is compared against this
const float min_sigma, // when background has suspiciously low stdev, this sigma kicks in
const unsigned min_peak_pixels, // if less than this number of pixels are considered part of peak, reject
const unsigned max_peak_pixels, // ditto but upper bound (count must be <=)
const unsigned max_peaks, // for buffer reasons
const float* image, // input data
unsigned int* output_counts,
float* output_x,
float* output_y,
......@@ -150,29 +155,28 @@ extern "C" __global__ void pf9(const unsigned short num_frames,
float peak_weighted_ss;
float peak_weighted_fs;
float peak_total_mass = 0;
unsigned num_peak_pixels = 1; // will expand from center pixel, count it already
{
/* TODO: more compact form */
float peak_weighted_ss_nom = 0;
float peak_weighted_fs_nom = 0;
// expand peak in rings
{
const float peak_pixel_threshold = mean + min_snr_peak_pixels * sigma;
for (unsigned short layer=1; layer<=window_radius; ++layer) {
float total_mass_before = peak_total_mass;
masked_frame.fun_ring(ss_index, fs_index, layer, [&] (unsigned short i, unsigned short j, float val) {
if (val > peak_pixel_threshold) {
float val_over_mean = val - mean;
peak_total_mass += val_over_mean;
peak_weighted_ss_nom += val_over_mean * static_cast<float>(i);
peak_weighted_fs_nom += val_over_mean * static_cast<float>(j);
}
});
// in case nothing was added, stop expanding
if (peak_total_mass == total_mass_before) {
break;
}
}
}
const float peak_pixel_threshold = mean + min_snr_peak_pixels * sigma;
for (unsigned short layer=1; layer<=window_radius; ++layer) {
unsigned num_peak_pixels_before = num_peak_pixels;
masked_frame.fun_ring(ss_index, fs_index, layer, [&] (unsigned short i, unsigned short j, float val) {
if (val > peak_pixel_threshold) {
float val_over_mean = val - mean;
peak_total_mass += val_over_mean;
peak_weighted_ss_nom += val_over_mean * static_cast<float>(i);
peak_weighted_fs_nom += val_over_mean * static_cast<float>(j);
++num_peak_pixels;
}
});
// in case nothing was added, stop expanding
if (num_peak_pixels == num_peak_pixels_before) {
break;
}
}
if (peak_total_mass <= mean + min_snr_whole_peak * sigma) {
return;
}
......
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