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Merge pull request #692 from dirac-institute/cleanups
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Remove some unused masking functions
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@jeremykubica
jeremykubica authored Sep 5, 2024
2 parents 4aefcc0 + dd4b0da commit b3f78c0
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Showing 5 changed files with 4 additions and 188 deletions.
6 changes: 4 additions & 2 deletions src/kbmod/configuration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,7 @@ def __str__(self):
result += f"{key}: {value}\n"
return result

def set(self, param, value):
def set(self, param, value, warn_on_unknown=False):
"""Sets the value of a specific parameter.
Parameters
Expand All @@ -96,8 +96,10 @@ def set(self, param, value):
The parameter name.
value : any
The parameter's value.
warn_on_unknown : `bool`
Generate a warning if the parameter is not known.
"""
if param not in self._params:
if warn_on_unknown and param not in self._params:
logger.warning(f"Setting unknown parameter: {param}")
self._params[param] = value

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67 changes: 0 additions & 67 deletions src/kbmod/search/layered_image.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -113,69 +113,6 @@ void LayeredImage::apply_mask(int flags) {
variance.apply_mask(flags, mask);
}

void LayeredImage::union_masks(RawImage& new_mask) {
const uint64_t num_pixels = get_npixels();
assert_sizes_equal(new_mask.get_width(), width, "global mask width");
assert_sizes_equal(new_mask.get_height(), height, "global mask height");

float* mask_pixels = mask.data();
float* new_pixels = new_mask.data();
for (uint64_t i = 0; i < num_pixels; ++i) {
int current_flags = static_cast<int>(mask_pixels[i]);
int new_flags = static_cast<int>(new_pixels[i]);

// Use a bitwise OR to keep flags set in the current pixel or the new mask.
mask_pixels[i] = current_flags | new_flags;
}
}

void LayeredImage::union_threshold_masking(float thresh) {
const uint64_t num_pixels = get_npixels();
float* sci_pixels = science.data();
float* mask_pixels = mask.data();

for (uint64_t i = 0; i < num_pixels; ++i) {
if (sci_pixels[i] > thresh) {
// Use a logical OR to preserve all other flags.
mask_pixels[i] = static_cast<int>(mask_pixels[i]) | 1;
}
}
}

/* This implementation of grow_mask is optimized for steps > 1
(which is how the code is generally used. If you are only
growing the mask by 1, the extra copy will be a little slower.
*/
void LayeredImage::grow_mask(int steps) {
logging::getLogger("kbmod.search.layered_image")
->debug("Growing mask by " + std::to_string(steps) + " steps.");

ImageI bitmask = ImageI::Constant(height, width, -1);
bitmask = (mask.get_image().array() > 0).select(0, bitmask);

for (int itr = 1; itr <= steps; ++itr) {
for (int j = 0; j < height; ++j) {
for (int i = 0; i < width; ++i) {
if (bitmask(j, i) == -1) {
if (((j - 1 >= 0) && (bitmask(j - 1, i) == itr - 1)) ||
((i - 1 >= 0) && (bitmask(j, i - 1) == itr - 1)) ||
((j + 1 < height) && (bitmask(j + 1, i) == itr - 1)) ||
((i + 1 < width) && (bitmask(j, i + 1) == itr - 1))) {
bitmask(j, i) = itr;
}
}
} // for i
} // for j
} // for step

// Overwrite the mask with the expanded one.
for (int j = 0; j < height; ++j) {
for (int i = 0; i < width; ++i) {
mask.set_pixel({j, i}, (bitmask(j, i) == -1) ? 0 : 1);
}
}
}

void LayeredImage::subtract_template(RawImage& sub_template) {
assert_sizes_equal(sub_template.get_width(), width, "template width");
assert_sizes_equal(sub_template.get_height(), height, "template height");
Expand Down Expand Up @@ -350,9 +287,6 @@ static void layered_image_bindings(py::module& m) {
})
.def("binarize_mask", &li::binarize_mask, pydocs::DOC_LayeredImage_binarize_mask)
.def("apply_mask", &li::apply_mask, pydocs::DOC_LayeredImage_apply_mask)
.def("union_masks", &li::union_masks, pydocs::DOC_LayeredImage_union_masks)
.def("union_threshold_masking", &li::union_threshold_masking,
pydocs::DOC_LayeredImage_union_threshold_masking)
.def("sub_template", &li::subtract_template, pydocs::DOC_LayeredImage_sub_template)
.def("get_science", &li::get_science, py::return_value_policy::reference_internal,
pydocs::DOC_LayeredImage_get_science)
Expand All @@ -365,7 +299,6 @@ static void layered_image_bindings(py::module& m) {
.def("set_variance", &li::set_variance, pydocs::DOC_LayeredImage_set_variance)
.def("convolve_psf", &li::convolve_psf, pydocs::DOC_LayeredImage_convolve_psf)
.def("convolve_given_psf", &li::convolve_given_psf, pydocs::DOC_LayeredImage_convolve_given_psf)
.def("grow_mask", &li::grow_mask, pydocs::DOC_LayeredImage_grow_mask)
.def("get_width", &li::get_width, pydocs::DOC_LayeredImage_get_width)
.def("get_height", &li::get_height, pydocs::DOC_LayeredImage_get_height)
.def("get_npixels", &li::get_npixels, pydocs::DOC_LayeredImage_get_npixels)
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3 changes: 0 additions & 3 deletions src/kbmod/search/layered_image.h
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Original file line number Diff line number Diff line change
Expand Up @@ -65,9 +65,6 @@ class LayeredImage {
// Masking functions.
void mask_pixel(const Index& idx);
void binarize_mask(int flags_to_keep);
void union_masks(RawImage& new_mask);
void union_threshold_masking(float thresh);
void grow_mask(int steps);
void apply_mask(int flags);

// Subtracts a template image from the science layer.
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30 changes: 0 additions & 30 deletions src/kbmod/search/pydocs/layered_image_docs.h
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Original file line number Diff line number Diff line change
Expand Up @@ -64,26 +64,6 @@ static const auto DOC_LayeredImage_apply_mask = R"doc(
call binarize_mask() first.
)doc";

static const auto DOC_LayeredImage_union_masks = R"doc(
Unions the masked pixel flags from the a given second mask layer onto
this image's mask layer. Modifies the mask layer in place.
Parameters
----------
global_mask : `RawImage`
The `RawImage` of global mask values (binary) for each pixel.
)doc";

static const auto DOC_LayeredImage_union_threshold_masking = R"doc(
Masks any pixel whose corresponding value in the science layer is
above the given threshold using mask flag = 1.
Parameters
----------
thresh : `float`
The threshold value to use.
)doc";

static const auto DOC_LayeredImage_sub_template = R"doc(
Subtract given image template
)doc";
Expand Down Expand Up @@ -127,16 +107,6 @@ static const auto DOC_LayeredImage_convolve_given_psf = R"doc(
The PSF to use.
)doc";

static const auto DOC_LayeredImage_grow_mask = R"doc(
Expands the NO_DATA tags to nearby pixels in the science and variance layers.
Modifies the images in-place.
Parameters
----------
steps : `int`
The number of pixels by which to grow the masked regions.
)doc";

static const auto DOC_LayeredImage_get_width = R"doc(
Returns the image's width in pixels.
)doc";
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86 changes: 0 additions & 86 deletions tests/test_layered_image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -215,60 +215,6 @@ def test_binarize_mask(self):
self.assertEqual(mask.get_pixel(10, 7), 1)
self.assertEqual(mask.get_pixel(10, 8), 0)

def test_union_masks(self):
# Mask out a range of pixels.
mask = self.image.get_mask()
mask.set_pixel(15, 12, 1)
mask.set_pixel(15, 13, 2)
mask.set_pixel(15, 14, 3)

mask2 = RawImage(mask.width, mask.height)
mask2.set_all(0.0)
mask2.set_pixel(15, 11, 1)
mask2.set_pixel(15, 13, 1)
mask2.set_pixel(15, 14, 1)
mask2.set_pixel(15, 15, 8)

self.image.union_masks(mask2)
self.assertEqual(mask.get_pixel(15, 10), 0)
self.assertEqual(mask.get_pixel(15, 11), 1) # bit 1 added
self.assertEqual(mask.get_pixel(15, 12), 1)
self.assertEqual(mask.get_pixel(15, 13), 3) # bit 1 added
self.assertEqual(mask.get_pixel(15, 14), 3)
self.assertEqual(mask.get_pixel(15, 15), 8)
self.assertEqual(mask.get_pixel(15, 16), 0)

def test_add_threshold_mask_flags(self):
masked_pixels = {}
threshold = 20.0

# Add an object brighter than the threshold.
add_fake_object(self.image, 50, 50, 500.0, self.p)

# Manually find all the pixels that should be masked.
science = self.image.get_science()
for y in range(self.image.get_height()):
for x in range(self.image.get_width()):
value = science.get_pixel(y, x)
if value > threshold:
index = self.image.get_width() * y + x
masked_pixels[index] = True
self.assertGreater(len(masked_pixels), 0)

# Reset the mask and perform threshold masking.
mask = self.image.get_mask()
mask.set_all(0.0)
self.image.union_threshold_masking(threshold)

# Check that we masked the correct pixels.
for y in range(self.image.get_height()):
for x in range(self.image.get_width()):
index = self.image.get_width() * y + x
if index in masked_pixels:
self.assertEqual(mask.get_pixel(y, x), 1)
else:
self.assertEqual(mask.get_pixel(y, x), 0)

def test_apply_mask(self):
# Nothing is initially masked.
science = self.image.get_science()
Expand All @@ -293,38 +239,6 @@ def test_apply_mask(self):
else:
self.assertTrue(science.pixel_has_data(y, x))

def test_grow_mask(self):
mask = self.image.get_mask()
mask.set_pixel(11, 10, 1)
mask.set_pixel(12, 10, 1)
mask.set_pixel(13, 10, 1)
self.image.grow_mask(1)

# Check that the mask has grown to all adjacent pixels.
for y in range(self.image.get_height()):
for x in range(self.image.get_width()):
should_mask = (
(x == 10 and y <= 14 and y >= 10)
or (x == 9 and y <= 13 and y >= 11)
or (x == 11 and y <= 13 and y >= 11)
)
self.assertEqual(mask.get_pixel(y, x) == 0, not should_mask)

def test_grow_mask_mult(self):
mask = self.image.get_mask()
mask.set_pixel(11, 10, 1)
mask.set_pixel(12, 10, 1)
self.image.grow_mask(3)

# Check that the mask has grown to all applicable pixels.
for y in range(self.image.get_height()):
for x in range(self.image.get_width()):
# Check whether the point is a manhattan distance of <= 3 from
# one of the original masked pixels.
dx = abs(x - 10)
dy = min(abs(y - 11), abs(y - 12))
self.assertEqual(mask.get_pixel(y, x) == 0, dx + dy > 3)

def test_psi_and_phi_image(self):
p = PSF(0.00000001) # A point function.
img = make_fake_layered_image(6, 5, 2.0, 4.0, 10.0, p)
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