lsst.scarlet.lite.models.free_form.FactorizedFreeFormComponent Class Reference
Inheritance diagram for lsst.scarlet.lite.models.free_form.FactorizedFreeFormComponent:
Public Member Functions | |
| __init__ (self, tuple bands, np.ndarray|Parameter spectrum, np.ndarray|Parameter morph, Box model_bbox, float|None bg_thresh=None, np.ndarray|None bg_rms=None, float floor=1e-20, list[tuple[int, int]]|None peaks=None, float min_area=0) | |
| np.ndarray | prox_spectrum (self, np.ndarray spectrum) |
| np.ndarray | prox_morph (self, np.ndarray morph) |
| bool | resize (self, Box model_box) |
| __str__ (self) | |
| __repr__ (self) | |
| np.ndarray | morph (self) |
| tuple[int, int]|None | peak (self) |
| tuple[int, int]|None | component_center (self) |
| np.ndarray | spectrum (self) |
| tuple | shape (self) |
| Image | get_model (self) |
| grad_spectrum (self, np.ndarray input_grad, np.ndarray spectrum, np.ndarray morph) | |
| grad_morph (self, np.ndarray input_grad, np.ndarray morph, np.ndarray spectrum) | |
| update (self, int it, np.ndarray input_grad) | |
| None | parameterize (self, Callable parameterization) |
| ScarletComponentBaseData | to_data (self) |
| Box | bbox (self) |
| tuple | bands (self) |
Public Attributes | |
| peaks = peaks | |
| min_area = min_area | |
| bg_rms = bg_rms | |
| bg_thresh = bg_thresh | |
| floor = floor | |
| monotonicity = monotonicity | |
| padding = padding | |
| is_symmetric = is_symmetric | |
| morph | |
Protected Attributes | |
| _spectrum = parameter(spectrum) | |
| _morph = parameter(morph) | |
| tuple[int, int]|None | _peak = peak |
| tuple | _bands = bands |
| Box | _bbox = bbox |
Detailed Description
Implements a free-form component
With no constraints this component is typically either a garbage collector,
or part of a set of components to deconvolve an image by separating out
the different spectral components.
See `FactorizedComponent` for a list of parameters not shown here.
Parameters
----------
peaks: `list` of `tuple`
A set of ``(cy, cx)`` peaks for detected sources.
If peak is not ``None`` then only pixels in the same "footprint"
as one of the peaks are included in the morphology.
If `peaks` is ``None`` then there is no constraint applied.
min_area: float
The minimum area for a peak.
If `min_area` is not `None` then all regions of the morphology
with fewer than `min_area` connected pixels are removed.
Definition at line 36 of file free_form.py.
Constructor & Destructor Documentation
◆ __init__()
| lsst.scarlet.lite.models.free_form.FactorizedFreeFormComponent.__init__ | ( | self, | |
| tuple | bands, | ||
| np.ndarray | Parameter | spectrum, | ||
| np.ndarray | Parameter | morph, | ||
| Box | model_bbox, | ||
| float | None | bg_thresh = None, | ||
| np.ndarray | None | bg_rms = None, | ||
| float | floor = 1e-20, | ||
| list[tuple[int, int]] | None | peaks = None, | ||
| float | min_area = 0 ) |
Definition at line 58 of file free_form.py.
69 ):
70 super().__init__(
71 bands=bands,
72 spectrum=spectrum,
73 morph=morph,
74 bbox=model_bbox,
75 peak=None,
76 bg_rms=bg_rms,
77 bg_thresh=bg_thresh,
78 floor=floor,
79 )
80
81 self.peaks = peaks
82 self.min_area = min_area
83
Member Function Documentation
◆ __repr__()
| lsst.scarlet.lite.models.free_form.FactorizedFreeFormComponent.__repr__ | ( | self | ) |
Definition at line 139 of file free_form.py.
139 def __repr__(self):
140 return self.__str__()
141
142
◆ __str__()
| lsst.scarlet.lite.models.free_form.FactorizedFreeFormComponent.__str__ | ( | self | ) |
Definition at line 132 of file free_form.py.
132 def __str__(self):
133 return (
134 f"FactorizedFreeFormComponent(\n bands={self.bands}\n "
135 f"spectrum={self.spectrum})\n center={self.peak}\n "
136 f"morph_shape={self.morph.shape}"
137 )
138
◆ bands()
|
inherited |
The bands in the component model
Definition at line 71 of file component.py.
71 def bands(self) -> tuple:
72 """The bands in the component model"""
73 return self._bands
74
◆ bbox()
|
inherited |
The bounding box that contains the component in the full image
Definition at line 66 of file component.py.
66 def bbox(self) -> Box:
67 """The bounding box that contains the component in the full image"""
68 return self._bbox
69
◆ component_center()
|
inherited |
The center of the component in its bounding box
This is likely to be different than `Component.center`,
since `Component.center` is the center of the component in the
full model, whereas `component_center` is the center of the component
inside its bounding box.
Returns
-------
center:
The center of the component in its bounding box
Definition at line 213 of file component.py.
213 def component_center(self) -> tuple[int, int] | None:
214 """The center of the component in its bounding box
215
216 This is likely to be different than `Component.center`,
217 since `Component.center` is the center of the component in the
218 full model, whereas `component_center` is the center of the component
219 inside its bounding box.
220
221 Returns
222 -------
223 center:
224 The center of the component in its bounding box
225 """
226 _center = self.peak
227 if _center is None:
228 return None
229 center = (
230 _center[0] - self.bbox.origin[-2],
231 _center[1] - self.bbox.origin[-1],
232 )
233 return center
234
◆ get_model()
|
inherited |
Build the model from the spectrum and morphology
Reimplemented from lsst.scarlet.lite.component.Component.
Definition at line 250 of file component.py.
250 def get_model(self) -> Image:
251 """Build the model from the spectrum and morphology"""
252 # The spectrum and morph might be Parameters,
253 # so cast them as arrays in the model.
254 spectrum = self.spectrum
255 morph = self.morph
256 model = spectrum[:, None, None] * morph[None, :, :]
258
◆ grad_morph()
|
inherited |
Gradient of the morph wrt. the component model
Definition at line 263 of file component.py.
263 def grad_morph(self, input_grad: np.ndarray, morph: np.ndarray, spectrum: np.ndarray):
264 """Gradient of the morph wrt. the component model"""
265 return np.einsum("i,i...", spectrum, input_grad)
266
◆ grad_spectrum()
|
inherited |
Gradient of the spectrum wrt. the component model
Definition at line 259 of file component.py.
259 def grad_spectrum(self, input_grad: np.ndarray, spectrum: np.ndarray, morph: np.ndarray):
260 """Gradient of the spectrum wrt. the component model"""
261 return np.einsum("...jk,jk", input_grad, morph)
262
◆ morph()
|
inherited |
The array of morphology values
Definition at line 241 of file component.py.
241 def morph(self) -> np.ndarray:
242 """The array of morphology values"""
243 return self._morph.x
244
◆ parameterize()
|
inherited |
Convert the component parameter arrays into Parameter instances
Parameters
----------
parameterization: Callable
A function to use to convert parameters of a given type into
a `Parameter` in place. It should take a single argument that
is the `Component` or `Source` that is to be parameterized.
Reimplemented from lsst.scarlet.lite.component.Component.
Definition at line 353 of file component.py.
353 def parameterize(self, parameterization: Callable) -> None:
354 """Convert the component parameter arrays into Parameter instances
355
356 Parameters
357 ----------
358 parameterization: Callable
359 A function to use to convert parameters of a given type into
360 a `Parameter` in place. It should take a single argument that
361 is the `Component` or `Source` that is to be parameterized.
362 """
363 # Update the spectrum and morph in place
364 parameterization(self)
365 # update the parameters
366 self._spectrum.grad = self.grad_spectrum
367 self._spectrum.prox = self.prox_spectrum
368 self._morph.grad = self.grad_morph
369 self._morph.prox = self.prox_morph
370
◆ peak()
|
inherited |
The peak of the component
Returns
-------
peak:
The peak of the component
Definition at line 202 of file component.py.
202 def peak(self) -> tuple[int, int] | None:
203 """The peak of the component
204
205 Returns
206 -------
207 peak:
208 The peak of the component
209 """
210 return self._peak
211
◆ prox_morph()
| np.ndarray lsst.scarlet.lite.models.free_form.FactorizedFreeFormComponent.prox_morph | ( | self, | |
| np.ndarray | morph ) |
Apply a prox-like update to the morphology This is the main difference between an `SedComponent` and a `FactorizedComponent`, since this component has fewer constraints.
Reimplemented from lsst.scarlet.lite.component.FactorizedComponent.
Definition at line 96 of file free_form.py.
96 def prox_morph(self, morph: np.ndarray) -> np.ndarray:
97 """Apply a prox-like update to the morphology
98
99 This is the main difference between an `SedComponent` and a
100 `FactorizedComponent`, since this component has fewer constraints.
101 """
102 from lsst.scarlet.lite.detect_pybind11 import get_connected_multipeak, get_footprints # type: ignore
103
104 if self.bg_thresh is not None and isinstance(self.bg_rms, np.ndarray):
105 bg_thresh = self.bg_rms * self.bg_thresh
106 # Enforce background thresholding
107 model = self.spectrum[:, None, None] * morph[None, :, :]
108 morph[np.all(model < bg_thresh[:, None, None], axis=0)] = 0
109 else:
110 # enforce positivity
111 morph[morph < 0] = 0
112
113 if self.peaks is not None:
114 footprint = get_connected_multipeak(morph, self.peaks, 0)
115 morph = morph * footprint
116
117 if self.min_area > 0:
119 bbox = self.bbox.copy()
120 bbox.origin = (0, 0)
121 footprint_image = footprints_to_image(footprints, bbox)
122 morph = morph * (footprint_image > 0).data
123
124 if np.all(morph == 0):
125 morph[0, 0] = self.floor
126
127 return morph
128
MatrixB get_connected_multipeak(py::EigenDRef< const M > image, const std::vector< std::vector< int > > ¢ers, const double thresh=0)
Proximal operator to trim pixels not connected to one of the source centers.
Definition detect_pybind11.cc:79
std::vector< Footprint > get_footprints(py::EigenDRef< const M > image, const double min_separation, const int min_area, const double peak_thresh, const double footprint_thresh, const bool find_peaks=true, const int y0=0, const int x0=0)
Get all footprints in an image.
Definition detect_pybind11.cc:309
◆ prox_spectrum()
| np.ndarray lsst.scarlet.lite.models.free_form.FactorizedFreeFormComponent.prox_spectrum | ( | self, | |
| np.ndarray | spectrum ) |
Apply a prox-like update to the spectrum This differs from `FactorizedComponent` because an `SedComponent` has the spectrum normalized to unity.
Reimplemented from lsst.scarlet.lite.component.FactorizedComponent.
Definition at line 84 of file free_form.py.
84 def prox_spectrum(self, spectrum: np.ndarray) -> np.ndarray:
85 """Apply a prox-like update to the spectrum
86
87 This differs from `FactorizedComponent` because an
88 `SedComponent` has the spectrum normalized to unity.
89 """
90 # prevent divergent spectrum
91 spectrum[spectrum < self.floor] = self.floor
92 # Normalize the spectrum
93 spectrum = spectrum / np.sum(spectrum)
94 return spectrum
95
◆ resize()
| bool lsst.scarlet.lite.models.free_form.FactorizedFreeFormComponent.resize | ( | self, | |
| Box | model_box ) |
Test whether or not the component needs to be resized
Reimplemented from lsst.scarlet.lite.component.FactorizedComponent.
Definition at line 129 of file free_form.py.
129 def resize(self, model_box: Box) -> bool:
130 return False
131
◆ shape()
|
inherited |
Shape of the resulting model image
Definition at line 246 of file component.py.
246 def shape(self) -> tuple:
247 """Shape of the resulting model image"""
248 return self.spectrum.shape + self.morph.shape
249
◆ spectrum()
|
inherited |
The array of spectrum values
Definition at line 236 of file component.py.
236 def spectrum(self) -> np.ndarray:
237 """The array of spectrum values"""
238 return self._spectrum.x
239
◆ to_data()
|
inherited |
Convert the component to persistable ScarletComponentBaseData
Returns
-------
component_data: ScarletComponentBaseData
The data object containing the component information
Reimplemented from lsst.scarlet.lite.component.Component.
Definition at line 371 of file component.py.
371 def to_data(self) -> ScarletComponentBaseData:
372 """Convert the component to persistable ScarletComponentBaseData
373
374 Returns
375 -------
376 component_data: ScarletComponentBaseData
377 The data object containing the component information
378 """
379 from .io import ScarletFactorizedComponentData
380
381 return ScarletFactorizedComponentData(
382 origin=self.bbox.origin, # type: ignore
383 peak=self.peak, # type: ignore
384 spectrum=self.spectrum,
385 morph=self.morph,
386 )
387
◆ update()
|
inherited |
Update the spectrum and morphology parameters
Reimplemented from lsst.scarlet.lite.component.Component.
Definition at line 345 of file component.py.
345 def update(self, it: int, input_grad: np.ndarray):
346 """Update the spectrum and morphology parameters"""
347 # Store the input spectrum so that the morphology can
348 # have a consistent update
349 spectrum = self.spectrum.copy()
350 self._spectrum.update(it, input_grad, self.morph)
351 self._morph.update(it, input_grad, spectrum)
352
Member Data Documentation
◆ _bands
|
protectedinherited |
Definition at line 62 of file component.py.
◆ _bbox
Definition at line 63 of file component.py.
◆ _morph
Definition at line 191 of file component.py.
◆ _peak
|
protectedinherited |
Definition at line 192 of file component.py.
◆ _spectrum
Definition at line 190 of file component.py.
◆ bg_rms
|
inherited |
Definition at line 193 of file component.py.
◆ bg_thresh
|
inherited |
Definition at line 194 of file component.py.
◆ floor
|
inherited |
Definition at line 196 of file component.py.
◆ is_symmetric
|
inherited |
Definition at line 199 of file component.py.
◆ min_area
| lsst.scarlet.lite.models.free_form.FactorizedFreeFormComponent.min_area = min_area |
Definition at line 82 of file free_form.py.
◆ monotonicity
|
inherited |
Definition at line 197 of file component.py.
◆ morph
|
inherited |
Definition at line 350 of file component.py.
◆ padding
|
inherited |
Definition at line 198 of file component.py.
◆ peaks
| lsst.scarlet.lite.models.free_form.FactorizedFreeFormComponent.peaks = peaks |
Definition at line 81 of file free_form.py.
The documentation for this class was generated from the following file:
- /j/snowflake/release/lsstsw/stack/lsst-scipipe-12.1.0/Linux/scarlet_lite/g00274db5b6+edbf708997/python/lsst/scarlet/lite/models/free_form.py
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