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Commit 0aeb426f authored by David Hammer's avatar David Hammer
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Merge branch '2025-winter-bud-fixes' into mid-arbiter-on-scene

parents d438abc7 74d39b40
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1 merge request!118Draft: MID: put arbiter on manager scene
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src/calng/Gotthard2Assembler.py
+ 7
− 0
View file @ 0aeb426f
......@@ -37,6 +37,13 @@ class Gotthard2Assembler(TrainMatcher.TrainMatcher):
.dataSchema(schemas.preview_schema(wrap_image_in_imagedata=False))
.commit(),
STRING_ELEMENT(expected)
.key("managerDevice")
.displayedName("Manager device")
.assignmentInternal()
.defaultValue("")
.commit(),
STRING_ELEMENT(expected)
.key("geometryDevice")
.displayedName("[Unused] Geometry device")
......
src/calng/frameselection_utils.py
+ 4
− 5
View file @ 0aeb426f
......@@ -138,9 +138,9 @@ class FrameselectionFriend:
def get_mask(self, sources):
if self._enabled and self._arbiter in sources:
return np.array(
sources[self._arbiter][0]["data.dataFramePattern"], copy=False
).astype(bool, copy=False)
return np.asarray(
sources[self._arbiter][0]["data.dataFramePattern"], dtype=bool
)
else:
return None
......@@ -171,8 +171,7 @@ class FrameselectionFriend:
if not arbiter.has(mask_key):
# no mask
continue
mask = np.array(
arbiter[mask_key], dtype=bool, copy=False)
mask = np.asarray(arbiter[mask_key], dtype=bool)
for source, data in correction_sources.items():
if not data.has(arg):
......
src/calng/kernels/peakfinder9_gpu.cu
+ 58
− 55
View file @ 0aeb426f
......@@ -4,15 +4,15 @@
class MaskedImageFrame {
public:
const float* data_start;
const unsigned short num_rows;
const unsigned short num_cols;
__device__ MaskedImageFrame(const float* data_start, const unsigned short num_rows, const unsigned short num_cols):
data_start(data_start), num_rows(num_rows), num_cols(num_cols) {}
const unsigned short ss_dim;
const unsigned short fs_dim;
__device__ MaskedImageFrame(const float* data_start, const unsigned short ss_dim, const unsigned short fs_dim):
data_start(data_start), ss_dim(ss_dim), fs_dim(fs_dim) {}
__device__ bool is_masked(const unsigned short i, const unsigned short j) {
return isnan(data_start[i * num_cols + j]);
return isnan(data_start[i * fs_dim + j]);
}
__device__ float get(const unsigned short i, const unsigned short j) {
return data_start[i * num_cols + j];
return data_start[i * fs_dim + j];
}
__device__ float get(const unsigned short i, const unsigned short j, const float fallback) {
if (is_masked(i, j)) {
......@@ -56,8 +56,8 @@ public:
};
extern "C" __global__ void pf9(const unsigned short num_frames,
const unsigned short num_rows,
const unsigned short num_cols,
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,
......@@ -73,37 +73,37 @@ extern "C" __global__ void pf9(const unsigned short num_frames,
// execution model: one thread handles one pixel in one frame
const unsigned short frame = blockDim.x * blockIdx.x + threadIdx.x;
const unsigned short row = blockDim.y * blockIdx.y + threadIdx.y;
const unsigned short col = blockDim.z * blockIdx.z + threadIdx.z;
const unsigned short ss_index = blockDim.y * blockIdx.y + threadIdx.y;
const unsigned short fs_index = blockDim.z * blockIdx.z + threadIdx.z;
if (frame >= num_frames ||
row < window_radius || row >= num_rows - window_radius ||
col < window_radius || col >= num_cols - window_radius) {
ss_index < window_radius || ss_index >= ss_dim - window_radius ||
fs_index < window_radius || fs_index >= fs_dim - window_radius) {
return;
}
// wrap thin helper class around for convenience
MaskedImageFrame masked_frame(image + frame * (num_rows * num_cols),
num_rows,
num_cols);
MaskedImageFrame masked_frame(image + frame * (ss_dim * fs_dim),
ss_dim,
fs_dim);
// candidate should not be masked
if (masked_frame.is_masked(row, col)) {
if (masked_frame.is_masked(ss_index, fs_index)) {
return;
}
float pixel_val = masked_frame.get(row, col);
float pixel_val = masked_frame.get(ss_index, fs_index);
// candidate should be greater than immediate neighbors
// with tie breaking: in case of equality, lowest row, col is candidate
if (pixel_val <= masked_frame.get(row-1, col-1, -INFINITY) ||
pixel_val <= masked_frame.get(row-1, col, -INFINITY) ||
pixel_val <= masked_frame.get(row-1, col+1, -INFINITY) ||
pixel_val <= masked_frame.get(row, col-1, -INFINITY) ||
pixel_val < masked_frame.get(row, col+1, -INFINITY) ||
pixel_val < masked_frame.get(row+1, col, -INFINITY) ||
pixel_val < masked_frame.get(row+1, col, -INFINITY) ||
pixel_val < masked_frame.get(row+1, col, -INFINITY)) {
// with tie breaking: in case of equality, lowest row, fs_index is candidate
if (pixel_val <= masked_frame.get(ss_index-1, fs_index-1, -INFINITY) ||
pixel_val <= masked_frame.get(ss_index-1, fs_index, -INFINITY) ||
pixel_val <= masked_frame.get(ss_index-1, fs_index+1, -INFINITY) ||
pixel_val <= masked_frame.get(ss_index, fs_index-1, -INFINITY) ||
pixel_val < masked_frame.get(ss_index, fs_index+1, -INFINITY) ||
pixel_val < masked_frame.get(ss_index+1, fs_index, -INFINITY) ||
pixel_val < masked_frame.get(ss_index+1, fs_index, -INFINITY) ||
pixel_val < masked_frame.get(ss_index+1, fs_index, -INFINITY)) {
return;
}
......@@ -112,7 +112,7 @@ extern "C" __global__ void pf9(const unsigned short num_frames,
// (full border for window radius 2, less for higher)
{
float border_max = -INFINITY;
masked_frame.fun_ring(row, col, window_radius, [&] (unsigned short, unsigned short, float val) {
masked_frame.fun_ring(ss_index, fs_index, window_radius, [&] (unsigned short, unsigned short, float val) {
border_max = max(border_max, val);
});
if (pixel_val - min_peak_over_border <= border_max) {
......@@ -127,7 +127,7 @@ extern "C" __global__ void pf9(const unsigned short num_frames,
// https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance#Welford's_online_algorithm
unsigned short count = 0;
float M2 = 0;
masked_frame.fun_ring(row, col, window_radius, [&] (unsigned short, unsigned short, float val) {
masked_frame.fun_ring(ss_index, fs_index, window_radius, [&] (unsigned short, unsigned short, float val) {
++count;
float delta = val - mean;
mean += delta / static_cast<float>(count);
......@@ -147,44 +147,47 @@ extern "C" __global__ void pf9(const unsigned short num_frames,
}
// whole peak should have sufficent SNR
float peak_weighted_row;
float peak_weighted_col;
float peak_total_mass = pixel_val - mean;
float peak_weighted_ss;
float peak_weighted_fs;
float peak_total_mass = 0;
{
/* TODO: more compact form */
float peak_weighted_row_nom = static_cast<float>(row) * pixel_val;
float peak_weighted_col_nom = static_cast<float>(col) * pixel_val;
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(row, col, 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_row_nom += val_over_mean * static_cast<float>(i);
peak_weighted_col_nom += val_over_mean * static_cast<float>(j);
}
});
// in case nothing was added, stop expanding
if (peak_total_mass == total_mass_before) {
break;
}
}
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;
}
}
}
if (peak_total_mass <= mean + min_snr_whole_peak * sigma) {
return;
}
if (peak_total_mass == 0) {
float peak_weighted_row = static_cast<float>(row);
float peak_weighted_col = static_cast<float>(col);
peak_weighted_ss = static_cast<float>(ss_index);
peak_weighted_fs = static_cast<float>(fs_index);
} else {
peak_weighted_row = peak_weighted_row_nom / peak_total_mass;
peak_weighted_col = peak_weighted_col_nom / peak_total_mass;
peak_weighted_ss = peak_weighted_ss_nom / peak_total_mass;
peak_weighted_fs = peak_weighted_fs_nom / peak_total_mass;
}
}
unsigned int output_index = atomicInc(output_counts + frame, max_peaks);
unsigned int output_pos = frame * max_peaks + output_index;
output_x[output_pos] = peak_weighted_row;
output_y[output_pos] = peak_weighted_col;
output_x[output_pos] = peak_weighted_ss;
output_y[output_pos] = peak_weighted_fs;
output_intensity[output_pos] = peak_total_mass;
}
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