Source code for tractor.engine

This file is part of the Tractor project.
Copyright 2011, 2012 Dustin Lang and David W. Hogg.
Licensed under the GPLv2; see the file COPYING for details.


Core image modeling and fitting.
from __future__ import print_function
import logging

import numpy as np

from astrometry.util.ttime import Time

from tractor.utils import MultiParams, _isint, get_class_from_name
from tractor.patch import Patch, ModelMask
from tractor.image import Image

def logverb(*args):
    msg = ' '.join([str(x) for x in args])

def logmsg(*args):
    msg = ' '.join([str(x) for x in args])

def isverbose():
    return (logging.getLogger().level <= logging.DEBUG)

def set_fp_err():
    '''Cause all floating-point errors to raise exceptions.
    Returns the current error state so you can revert via:

        olderr = set_fp_err()
        # do stuff
    return np.seterr(all='raise')

[docs]class Catalog(MultiParams): ''' A list of Source objects. This class allows the Tractor to treat a set of astronomical sources as a single object with a bunch of parameters. Most of the functionality comes from the base class. Constructor syntax: cat = Catalog(src1, src2, src3) so if you have a list of sources, srcs = [src1, src2, src3] cat = Catalog(*srcs) ''' deepcopy = MultiParams.copy def __str__(self): return ('Catalog: %i sources, %i parameters' % (len(self), self.numberOfParams()))
[docs] def printLong(self): print('Catalog with %i sources:' % len(self)) for i, x in enumerate(self): print(' %i:' % i, x)
[docs] def getThawedSources(self): return self._getActiveSubs()
[docs] def getFrozenSources(self): return self._getInactiveSubs()
[docs] def getNamedParamName(self, j): return 'source%i' % j
[docs]class Images(MultiParams): """ This is a class for holding a list of `Image` objects, each which contains data and metadata. This class allows the Tractor to treat a list of `Image`s as a single object that has a set of parameters. Basically all the functionality comes from the base class. """
[docs] def getNamedParamName(self, j): return 'image%i' % j
class OptResult(): # quack pass
[docs]class Tractor(MultiParams): ''' Heavy farm machinery. As you might guess from the name, this is the main class of the Tractor framework. A Tractor has a set of Images and a set of Sources, and has methods to optimize the parameters of those Images and Sources. ''' @staticmethod
[docs] def getName(): return 'Tractor'
[docs] def getNamedParams(): return dict(images=0, catalog=1)
def __init__(self, images=[], catalog=[], optimizer=None): ''' - `images:` list of Image objects (data) - `catalog:` list of Source objects ''' if not isinstance(images, Images): images = Images(*images) if not isinstance(catalog, Catalog): catalog = Catalog(*catalog) super(Tractor, self).__init__(images, catalog) self.modtype = np.float32 self.modelMasks = None self.expectModelMasks = False if optimizer is None: from .lsqr_optimizer import LsqrOptimizer self.optimizer = LsqrOptimizer() else: self.optimizer = optimizer def __str__(self): s = ('%s with %i sources and %i images' % ( self.getName(), len(self.catalog), len(self.images))) names = [] for im in self.images: if is None: names.append('[unnamed]') else: names.append( s += ' (' + ', '.join(names) + ')' return s # For use from emcee def __call__(self, X): self.setParams(X) return self.getLogProb() # For pickling def __getstate__(self): version = 1 S = (version, self.getImages(), self.getCatalog(), self.liquid, self.modtype, self.modelMasks, self.expectModelMasks, self.optimizer) return S def __setstate__(self, state): if len(state) == 6: # "backwards compat" (images, catalog, self.liquid, self.modtype, self.modelMasks, self.expectModelMasks) = state from .lsqr_optimizer import LsqrOptimizer self.optimizer = LsqrOptimizer() elif len(state) == 8: (ver, images, catalog, self.liquid, self.modtype, self.modelMasks, self.expectModelMasks, self.optimizer) = state self.subs = [images, catalog]
[docs] def getNImages(self): return len(self.images)
[docs] def getImage(self, imgi): return self.images[imgi]
[docs] def getImages(self): return self.images
[docs] def getCatalog(self): return self.catalog
[docs] def setCatalog(self, srcs): # FIXME -- ensure that "srcs" is a Catalog? Or duck-type it? self.catalog = srcs
[docs] def setImages(self, ims): self.images = ims
[docs] def addImage(self, img): self.images.append(img)
[docs] def addSource(self, src): self.catalog.append(src)
[docs] def addSources(self, srcs): self.catalog.extend(srcs)
[docs] def removeSource(self, src): self.catalog.remove(src)
[docs] def optimize_forced_photometry(self, **kwargs): ''' Returns an "OptResult" duck with fields: .ims0, .ims1 (if wantims=True) .IV (if variance=True) .fitstats (if fitstats=True) ims0, ims1: [ (img_data, mod, ie, chi, roi), ... ] ASSUMES linear brightnesses! ASSUMES all source parameters except brightness are frozen. If sky=False, ASSUMES image parameters are frozen. If sky=True, ASSUMES only the sky parameters are unfrozen ASSUMES the PSF and Sky models are position-independent!! PRIORS probably don't work because we don't setParams() when evaluating likelihood or prior! ''' return self.optimizer.forced_photometry(self, **kwargs)
# alphas=None, damp=0, priors=True, scale_columns=True, # shared_params=True, variance=False, just_variance=False):
[docs] def optimize(self, **kwargs): ''' Performs *one step* of optimization. (Exactly what that entails depends on the optimizer; by default (LsqrOptimizer) it means one linearized least-squares + line search iteration.) Returns (delta-logprob, parameter update X, alpha stepsize) If variance=True, Returns (delta-logprob, parameter update X, alpha stepsize, variance) If just_variance=True, Returns variance. ''' ''' If rois is not None, it must be a list of [x0,x1,y0,y1] the same length as the number of images, giving the ROI in which the chi value (and derivatives) will be evaluated. ''' return self.optimizer.optimize(self, **kwargs)
[docs] def optimize_loop(self, **kwargs): ''' Performs multiple steps of optimization until convergence. Returns a dict of results (exact contents varying by optimizer). ''' return self.optimizer.optimize_loop(self, **kwargs)
[docs] def getDerivs(self): ''' Computes model-image derivatives for each parameter. Returns a nested list of tuples: allderivs: [ (param0:) [ (deriv, img), (deriv, img), ... ], (param1:) [], (param2:) [ (deriv, img), ], ] Where the *derivs* are *Patch* objects and *imgs* are *Image* objects. ''' allderivs = [] if self.isParamFrozen('catalog'): srcs = [] else: srcs = list(self.catalog.getThawedSources()) allsrcs = self.catalog if not self.isParamFrozen('images'): for i in self.images.getThawedParamIndices(): img = self.images[i] derivs = img.getParamDerivatives(self, allsrcs) mod0 = None for di, deriv in enumerate(derivs): if deriv is False: if mod0 is None: mod0 = self.getModelImage(img) p0 = img.getParams() stepsizes = img.getStepSizes() paramnames = img.getParamNames() oldval = img.setParam(di, p0[di] + stepsizes[di]) mod = self.getModelImage(img) img.setParam(di, oldval) deriv = Patch(0, 0, (mod - mod0) / stepsizes[di]) = 'd(im%i)/d(%s)' % (i, paramnames[di]) allderivs.append([(deriv, img)]) del mod0 for src in srcs: srcderivs = [[] for i in range(src.numberOfParams())] for img in self.images: derivs = self._getSourceDerivatives(src, img) for k, deriv in enumerate(derivs): if deriv is None: continue srcderivs[k].append((deriv, img)) allderivs.extend(srcderivs) #print('allderivs:', len(allderivs)) #print('N params:', self.numberOfParams()) assert(len(allderivs) == self.numberOfParams()) return allderivs
[docs] def setModelMasks(self, masks, assumeMasks=True): ''' A "model mask" is used to define the pixels that are evaluated when computing the model patch for a source in an image. This allows for consistent computation of derivatives and optimization, without introducing errors due to approximating the profiles differently given different parameter settings. *masks*: if None, this masking is disabled, and normal approximation rules apply. Otherwise, *masks* must be a list, with length equal to the number of images. Each list element must be a dictionary with Source objects for keys and ModelMask objects for values. Sources that do not touch the image should not exist in the dictionary; all the ModelMask objects should be non-None and non-empty. ''' self.modelMasks = masks assert((masks is None) or (len(masks) == len(self.images))) self.expectModelMasks = (masks is not None) and assumeMasks
def _getModelMaskFor(self, image, src): if self.modelMasks is None: return None i = self.images.index(image) try: return self.modelMasks[i][src] except KeyError: return None def _checkModelMask(self, patch, mask): if self.expectModelMasks: if patch is not None: assert(mask is not None) if patch is not None and mask is not None: # not strictly required? but a good idea! assert(patch.patch.shape == mask.patch.shape) if patch is not None and mask is not None and patch.patch is not None: nonzero = Patch(patch.x0, patch.y0, patch.patch != 0) #print('nonzero type:', nonzero.patch.dtype) unmasked = Patch(mask.x0, mask.y0, np.logical_not(mask.mask)) #print('unmasked type:', unmasked.patch.dtype) bad = nonzero.performArithmetic(unmasked, '__iand__', otype=bool) assert(np.all(bad.patch == False)) def _getSourceDerivatives(self, src, img, **kwargs): mask = self._getModelMaskFor(img, src) # HACK! -- assume no modelMask -> no overlap if self.expectModelMasks and mask is None: return [None] * src.numberOfParams() derivs = src.getParamDerivatives(img, modelMask=mask, **kwargs) # HACK -- auto-add? # if self.expectModelMasks: # for d in derivs: # if d is not None and mask is None: # # add to modelMasks # i = self.images.index(img) # # set 'mask' so the assertion in _checkModelMask doesn't fire # mask = Patch(d.x0, d.y0, d.patch != 0) # self.modelMasks[i][src] = mask # HACK -- check 'em # for d in derivs: # if d is not None: # self._checkModelMask(d, mask) return derivs
[docs] def getModelPatch(self, img, src, **kwargs): mask = self._getModelMaskFor(img, src) # HACK -- assume no mask -> no overlap if self.expectModelMasks and mask is None: return None mod = src.getModelPatch(img, modelMask=mask, **kwargs) return mod
[docs] def getModelImage(self, img, srcs=None, sky=True, minsb=None): ''' Create a model image for the given "tractor image", including the sky level. If "srcs" is specified (a list of sources), then only those sources will be rendered into the image. Otherwise, the whole catalog will be. ''' if _isint(img): img = self.getImage(img) mod = np.zeros(img.getModelShape(), self.modtype) if sky: img.getSky().addTo(mod) if srcs is None: srcs = self.catalog for src in srcs: if src is None: continue patch = self.getModelPatch(img, src, minsb=minsb) if patch is None: continue patch.addTo(mod) return mod
[docs] def getModelImages(self, **kwargs): for img in self.images: yield self.getModelImage(img, **kwargs)
[docs] def getChiImages(self): for img in self.images: yield self.getChiImage(img=img)
[docs] def getChiImage(self, imgi=-1, img=None, srcs=None, minsb=0.): if img is None: img = self.getImage(imgi) mod = self.getModelImage(img, srcs=srcs, minsb=minsb) chi = (img.getImage() - mod) * img.getInvError() if not np.all(np.isfinite(chi)): print('Chi not finite') print('Image finite?', np.all(np.isfinite(img.getImage()))) print('Mod finite?', np.all(np.isfinite(mod))) print('InvErr finite?', np.all(np.isfinite(img.getInvError()))) print('Current thawed parameters:') self.printThawedParams() print('Current sources:') for src in self.getCatalog(): print(' ', src) print('Image:', img) print('sky:', img.getSky()) print('psf:', img.getPsf()) return chi
[docs] def getLogLikelihood(self): chisq = 0. for i, chi in enumerate(self.getChiImages()): chisq += (chi.astype(float) ** 2).sum() return -0.5 * chisq
[docs] def getLogProb(self): ''' Return the posterior log PDF, evaluated at the current parameters. ''' lnprior = self.getLogPrior() if lnprior == -np.inf: return lnprior lnl = self.getLogLikelihood() lnp = lnprior + lnl if np.isnan(lnp): print('Tractor.getLogProb() returning NaN.') print('Params:') self.printThawedParams() print('log likelihood:', lnl) print('log prior:', lnprior) return -np.inf return lnp